[PyMOL] Editing of the pdb structure

[James Starlight]

Dear PyMol Users!



Recently I've opened such topic but I didnt obtain answer on this question
so I try to paraphrase my task. Also I want to specify this topic on
questions lincked with the processing of pdbs.

1) I need to remove some elements fron my structure described as the
individual residue and place another element of the same size on the place
of the first element.

In particular I have two different peptides both of wich have small cap
groups on C and N termi. ( attached)

I need to remove all caps ( two caps FOR and ETA because there are two
identical chains in that structure) from the 1MAG structure and build
exactly on this place another cap groups wich I'd like to copy from the
second peptide ( KALP). So I'd like to change FOR- > ACE and ETA-> NH2
twisely for the 1MAG dtructure

How I can perform such task in PyMol?

James

[Thomas Holder]

Hi James,

> Recently I've opened such topic but I didnt obtain answer on this
> question so I try to paraphrase my task. Also I want to specify this
> topic on questions lincked with the processing of pdbs.
>
> 1) I need to remove some elements fron my structure described as the
> individual residue and place another element of the same size on the
> place of the first element.
>
> In particular I have two different peptides both of wich have small cap
> groups on C and N termi. ( attached)
>
> I need to remove all caps ( two caps FOR and ETA because there are two
> identical chains in that structure) from the 1MAG structure and build
> exactly on this place another cap groups wich I'd like to copy from the
> second peptide ( KALP).

the "Mutagenesis Wizard" comes in handy for editing caps. However it
fails with non-standard amino acis as far as I know. Then you have to do
it manually.

These commands could be a good start for your task:
http://pymolwiki.org/index.php/Remove
http://pymolwiki.org/index.php/Fuse

> So I'd like to change FOR- > ACE and ETA-> NH2
> twisely for the 1MAG dtructure

hm, shouldn't it be the other way round? FOR is N-terminus and ETA is
C-terminus?

Cheers,
Thomas

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

[Joel Tyndall]

Hi James,

If I am correct in reading what you want you wish to change the FOR group to an ACE.

I am using a PC version 1.3. Click on the builder button (right hand side of grey GUI)
Make sure you are in Mouse mode: 3 button editing.

Click on the carbon of the FOR group and also the oxygen ( a white ball will appear on each atom)
Then in the GUI click on the || icon adjacent to "bonds create". This will give you the carbonyl.
Now click on the hydrogen attached to the carbonyl carbon and then click in the GUI, the carbon atom C.
This has now created your Acetylated nitrogen.

Then save molecule as: and you can edit the text file to change For to ACE.

Given this is some sort of dimer, I have just noticed that the second chain will overlap with the first.

Hope this helps

Joel

From: James Starlight [mailto:***@gmail.com]
Sent: Friday, 11 November 2011 1:44 a.m.
To: pymol-***@lists.sourceforge.net
Subject: [PyMOL] Editing of the pdb structure

Dear PyMol Users!



Recently I've opened such topic but I didnt obtain answer on this question so I try to paraphrase my task. Also I want to specify this topic on questions lincked with the processing of pdbs.

1) I need to remove some elements fron my structure described as the individual residue and place another element of the same size on the place of the first element.

In particular I have two different peptides both of wich have small cap groups on C and N termi. ( attached)

I need to remove all caps ( two caps FOR and ETA because there are two identical chains in that structure) from the 1MAG structure and build exactly on this place another cap groups wich I'd like to copy from the second peptide ( KALP). So I'd like to change FOR- > ACE and ETA-> NH2 twisely for the 1MAG dtructure

How I can perform such task in PyMol?

James

[James Starlight]

Dear all! :)

I need to merge two chains in one pdb ( object) into one united chain. How
I could do it?

Thanks

James

2011/11/18 Joel Tyndall <***@otago.ac.nz>

> James,****
>
> ** **
>
> Please post this to the bulletin board. You can try to click on the word
> (residues usually default) at the bottom right of the viewer.****
>
> ** **
>
> Joel****
>
> ** **
>
> *From:* James Starlight [mailto:***@gmail.com]
> *Sent:* Thursday, 17 November 2011 7:52 a.m.
>
> *To:* Joel Tyndall
> *Subject:* Re: [PyMOL] Editing of the pdb structure****
>
> ** **
>
> Another question about working with the structure.
>
>
> I have structure of the fulerene molecule wich consist of 60 carbon atoms
>
> I switch to the Sequence mode-> Atoms and try to select individual carbon
> atoms ( e.g I want to find where this atom situated in my molecule). But
> instead of selection of the individual carbons the whole molecule was
> selected. How I can work with individual atoms of my structure ?
>
> James****
>
> 2011/11/15 James Starlight <***@gmail.com>****
>
> Thanks Joel, it's clear now :)****
>
> ** **
>
> 2011/11/14 Joel Tyndall <***@otago.ac.nz>****
>
> See attached.****
>
> ****
>
> To switch to editing mode click on 3 button viewing or use the menu****
>
> ****
>
> Mouse > 3 button editing****
>
> ****
>
> ****
>
> ****
>
> ****
>
> ****
>
> *From:* James Starlight [mailto:***@gmail.com]
> *Sent:* Monday, 14 November 2011 8:44 p.m.
> *To:* Joel Tyndall
> *Subject:* Re: [PyMOL] Editing of the pdb structure****
>
> ****
>
> Dear all, thank you for the advises :)
>
> Thomas,
>
> when I've tried to add ACE cap to the N-tem of the first residue of my
> peptide I've obtain
>
> Error: unable to load fragment ''.
>
> So how I should define dirr from wich those caps groups will be loaded?
>
>
> Joel,
>
> I could not find such buiilder button :o
>
> when I've tried to select individual atoms from my FOR residue ( from
> sequence panell), the overal residue with all atoms was selected instead :o
>
> James****
>
> 2011/11/11 Joel Tyndall <***@otago.ac.nz>****
>
> Hi James,****
>
> ****
>
> If I am correct in reading what you want you wish to change the FOR group
> to an ACE.****
>
> ****
>
> I am using a PC version 1.3. Click on the builder button (right hand side
> of grey GUI)****
>
> Make sure you are in Mouse mode: 3 button editing.****
>
> ****
>
> Click on the carbon of the FOR group and also the oxygen ( a white ball
> will appear on each atom)****
>
> Then in the GUI click on the || icon adjacent to “bonds create”. This will
> give you the carbonyl.****
>
> Now click on the hydrogen attached to the carbonyl carbon and then click
> in the GUI, the carbon atom C.****
>
> This has now created your Acetylated nitrogen.****
>
> ****
>
> Then save molecule as: and you can edit the text file to change For to ACE.
> ****
>
> ****
>
> Given this is some sort of dimer, I have just noticed that the second
> chain will overlap with the first.****
>
> ****
>
> Hope this helps****
>
> ****
>
> Joel ****
>
> ****
>
> *From:* James Starlight [mailto:***@gmail.com]
> *Sent:* Friday, 11 November 2011 1:44 a.m.
> *To:* pymol-***@lists.sourceforge.net
> *Subject:* [PyMOL] Editing of the pdb structure****
>
> ****
>
> Dear PyMol Users!
>
>
>
> Recently I've opened such topic but I didnt obtain answer on this question
> so I try to paraphrase my task. Also I want to specify this topic on
> questions lincked with the processing of pdbs.
>
> 1) I need to remove some elements fron my structure described as the
> individual residue and place another element of the same size on the place
> of the first element.
>
> In particular I have two different peptides both of wich have small cap
> groups on C and N termi. ( attached)
>
> I need to remove all caps ( two caps FOR and ETA because there are two
> identical chains in that structure) from the 1MAG structure and build
> exactly on this place another cap groups wich I'd like to copy from the
> second peptide ( KALP). So I'd like to change FOR- > ACE and ETA-> NH2
> twisely for the 1MAG dtructure
>
> How I can perform such task in PyMol?
>
> James****
>
> ****
>
> ** **
>
> ** **
>

[Jason Vertrees]

James,

Please look up the 'create' (http://www.pymolwiki.org/index.php/Create) comand.

Cheers,

-- Jason

On Sat, Nov 26, 2011 at 6:17 AM, James Starlight <***@gmail.com> wrote:
> Dear all! :)
>
> I need to merge two chains in one pdb ( object) into one united chain. How I
> could do it?
>
> Thanks
>
> James
>
> 2011/11/18 Joel Tyndall <***@otago.ac.nz>
>>
>> James,
>>
>>
>>
>> Please post this to the bulletin board. You can try to click on the word
>> (residues usually default) at the bottom right of the viewer.
>>
>>
>>
>> Joel
>>
>>
>>
>> From: James Starlight [mailto:***@gmail.com]
>> Sent: Thursday, 17 November 2011 7:52 a.m.
>>
>> To: Joel Tyndall
>> Subject: Re: [PyMOL] Editing of the pdb structure
>>
>>
>>
>> Another question about working with the structure.
>>
>>
>> I have structure of the fulerene molecule wich consist of 60 carbon atoms
>>
>> I switch to the Sequence mode-> Atoms and try to select individual carbon
>> atoms ( e.g I want to find where this atom situated in my molecule). But
>> instead of selection of the individual carbons the whole molecule was
>> selected. How I can work with individual atoms of my structure ?
>>
>> James
>>
>> 2011/11/15 James Starlight <***@gmail.com>
>>
>> Thanks Joel, it's clear now :)
>>
>>
>>
>> 2011/11/14 Joel Tyndall <***@otago.ac.nz>
>>
>> See attached.
>>
>>
>>
>> To switch to editing mode click on 3 button viewing or use the menu
>>
>>
>>
>> Mouse > 3 button editing
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> From: James Starlight [mailto:***@gmail.com]
>> Sent: Monday, 14 November 2011 8:44 p.m.
>> To: Joel Tyndall
>> Subject: Re: [PyMOL] Editing of the pdb structure
>>
>>
>>
>> Dear all, thank you for the advises :)
>>
>> Thomas,
>>
>> when I've tried to add ACE cap to the N-tem of the first residue of my
>> peptide I've obtain
>>
>> Error: unable to load fragment ''.
>>
>> So how I should define dirr from wich those caps groups will be loaded?
>>
>>
>> Joel,
>>
>> I could not find such buiilder button :o
>>
>> when I've tried to select individual atoms from my FOR residue ( from
>> sequence panell), the overal residue with all atoms was selected instead :o
>>
>> James
>>
>> 2011/11/11 Joel Tyndall <***@otago.ac.nz>
>>
>> Hi James,
>>
>>
>>
>> If I am correct in reading what you want you wish to change the FOR group
>> to an ACE.
>>
>>
>>
>> I am using a PC version 1.3. Click on the builder button (right hand side
>> of grey GUI)
>>
>> Make sure you are in Mouse mode: 3 button editing.
>>
>>
>>
>> Click on the carbon of the FOR group and also the oxygen ( a white ball
>> will appear on each atom)
>>
>> Then in the GUI click on the || icon adjacent to “bonds create”. This will
>> give you the carbonyl.
>>
>> Now click on the hydrogen attached to the carbonyl carbon and then click
>> in the GUI, the carbon atom C.
>>
>> This has now created your Acetylated nitrogen.
>>
>>
>>
>> Then save molecule as: and you can edit the text file to change For to
>> ACE.
>>
>>
>>
>> Given this is some sort of dimer, I have just noticed that the second
>> chain will overlap with the first.
>>
>>
>>
>> Hope this helps
>>
>>
>>
>> Joel
>>
>>
>>
>> From: James Starlight [mailto:***@gmail.com]
>> Sent: Friday, 11 November 2011 1:44 a.m.
>> To: pymol-***@lists.sourceforge.net
>> Subject: [PyMOL] Editing of the pdb structure
>>
>>
>>
>> Dear PyMol Users!
>>
>>
>>
>> Recently I've opened such topic but I didnt obtain answer on this question
>> so I try to paraphrase my task. Also I want to specify this topic on
>> questions lincked with the processing of pdbs.
>>
>> 1) I need to remove some elements fron my structure described as the
>> individual residue and place another element of the same size on the place
>> of the first element.
>>
>> In particular I have two  different peptides both of wich have small cap
>> groups on C and N termi. ( attached)
>>
>> I need to remove all caps ( two caps FOR and ETA because there are two
>> identical chains in that structure) from the 1MAG structure and build
>> exactly on this place another cap groups wich I'd like to copy from the
>> second peptide ( KALP). So I'd like to change FOR- > ACE and ETA-> NH2
>> twisely for the 1MAG dtructure
>>
>> How I can perform such task in PyMol?
>>
>> James
>>
>>
>>
>>
>>
>>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> PyMOL-users mailing list (PyMOL-***@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-***@lists.sourceforge.net
>



--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) ***@schrodinger.com
(o) [phone]

[James Starlight]

Deal all!

I'm intresting about representation of the polarr contacts between ligand
and protein

1) Usually I'm ussing Present-> Ligand sites option for that purposes but
in my current case I'm working with GFP where tree residues form chromofore
group of that protein.

So I want to assign that three residues as the ligand and finally find
polar contacts between that chromophore and surrounding polar residues. How
I could do this assignment?

2) Also I'm looking in possible way to represent Names of residues wich
forrm my ligand binding pocket. Always I represent names of residues via
Label option. But if I choose Label -> res.names all names will be
represented but i want to represent only the names of residues wich form
polar contact with ligand.

James


2012/1/10 Jason Vertrees <***@schrodinger.com>

> James,
>
> Please take these questions to the pymol-users list. I'm getting ready
> for the PyMOL v1.5 release, so you'll get faster answers there.
>
> Cheers,
>
> -- Jason
>
> On Tue, Jan 10, 2012 at 6:22 AM, James Starlight <***@gmail.com>
> wrote:
> > Hi Jason
> >
> > Thank you for help again.
> >
> > I've also question about representation of the polarr contacts between
> > ligand and protein
> >
> > Usually I'm ussing Present-> Ligand sites option for that purposes but
> in my
> > current case I'm working with GFP where tree residues form chromofore
> group
> > of that protein.
> >
> > So I want to assign that three residues as the ligand and finally find
> polar
> > contacts between that chromophore and surrounding polar residues. How I
> > could do this assignment?
> >
> > Thanks again
> >
> > James
> >
> >
> > 2012/1/9 Jason Vertrees <***@schrodinger.com>
> >>
> >> Hi James,
> >>
> >> I see you want chains A and B in one object to become just chain AA,
> >> for example, in another object? If so,
> >>
> >> create newObj, (oldObj1 and chain A) or (oldObj2 and chain B)
> >>
> >> alter newObj, chain=AA
> >>
> >> Cheers,
> >>
> >> -- Jason
> >>
> >> On Mon, Jan 9, 2012 at 2:26 AM, James Starlight <***@gmail.com
> >
> >> wrote:
> >> > Jason hello!
> >> >
> >> > I've tried exactly that command with OR operator
> >> >
> >> > but new object consitsted of 2 different chains like initial
> structure (
> >> > this was equal to the simple coppy of the 2g16 to the 2g16new object
> >> > without
> >> > deleation of initial one). But I want that 2g16new will consist of
> only
> >> > 1
> >> > chain wich would contait residues from both A and B of initial object.
> >> >
> >> > James
> >> >
> >> >>
> >> >> Cheers,
> >> >>
> >> >> -- JAson
> >> >>
> >> >> On Sun, Jan 8, 2012 at 1:35 AM, James Starlight
> >> >> <***@gmail.com>
> >> >> wrote:
> >> >> > Jason hello!
> >> >> >
> >> >> > I've tried use Create command to merge 2 chains from one object
> into
> >> >> > the united chain in new object but failed.
> >> >> >
> >> >> > create 2g16new, 2g16 and chain A 2g16 and chain B
> >> >> >
> >> >> > It's because of my new object also consist of 2 chains ( like
> >> >> > initial
> >> >> > one) but I want to obtain new object only with one chain wich would
> >> >> > consist of atoms from both chains of initial object. ( A+B)
> >> >> >
> >> >> > How I could solve that problem?
> >> >> >
> >> >> > James
> >> >> >
> >> >> > 2011/11/27, Jason Vertrees <***@schrodinger.com>:
> >> >> >> James,
> >> >> >>
> >> >> >> Please look up the 'create'
> >> >> >> (http://www.pymolwiki.org/index.php/Create)
> >> >> >> comand.
> >> >> >>
> >> >> >> Cheers,
> >> >> >>
> >> >> >> -- Jason
> >> >> >>
> >> >> >> On Sat, Nov 26, 2011 at 6:17 AM, James Starlight
> >> >> >> <***@gmail.com>
> >> >> >> wrote:
> >> >> >>> Dear all! :)
> >> >> >>>
> >> >> >>> I need to merge two chains in one pdb ( object) into one united
> >> >> >>> chain.
> >> >> >>> How
> >> >> >>> I
> >> >> >>> could do it?
> >> >> >>>
> >> >> >>> Thanks
> >> >> >>>
> >> >> >>> James
> >> >> >>>
> >> >> >>> 2011/11/18 Joel Tyndall <***@otago.ac.nz>
> >> >> >>>>
> >> >> >>>> James,
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Please post this to the bulletin board. You can try to click on
> >> >> >>>> the
> >> >> >>>> word
> >> >> >>>> (residues usually default) at the bottom right of the viewer.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Joel
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> From: James Starlight [mailto:***@gmail.com]
> >> >> >>>> Sent: Thursday, 17 November 2011 7:52 a.m.
> >> >> >>>>
> >> >> >>>> To: Joel Tyndall
> >> >> >>>> Subject: Re: [PyMOL] Editing of the pdb structure
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Another question about working with the structure.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> I have structure of the fulerene molecule wich consist of 60
> >> >> >>>> carbon
> >> >> >>>> atoms
> >> >> >>>>
> >> >> >>>> I switch to the Sequence mode-> Atoms and try to select
> individual
> >> >> >>>> carbon
> >> >> >>>> atoms ( e.g I want to find where this atom situated in my
> >> >> >>>> molecule).
> >> >> >>>> But
> >> >> >>>> instead of selection of the individual carbons the whole
> molecule
> >> >> >>>> was
> >> >> >>>> selected. How I can work with individual atoms of my structure ?
> >> >> >>>>
> >> >> >>>> James
> >> >> >>>>
> >> >> >>>> 2011/11/15 James Starlight <***@gmail.com>
> >> >> >>>>
> >> >> >>>> Thanks Joel, it's clear now :)
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> 2011/11/14 Joel Tyndall <***@otago.ac.nz>
> >> >> >>>>
> >> >> >>>> See attached.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> To switch to editing mode click on 3 button viewing or use the
> >> >> >>>> menu
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Mouse > 3 button editing
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> From: James Starlight [mailto:***@gmail.com]
> >> >> >>>> Sent: Monday, 14 November 2011 8:44 p.m.
> >> >> >>>> To: Joel Tyndall
> >> >> >>>> Subject: Re: [PyMOL] Editing of the pdb structure
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Dear all, thank you for the advises :)
> >> >> >>>>
> >> >> >>>> Thomas,
> >> >> >>>>
> >> >> >>>> when I've tried to add ACE cap to the N-tem of the first residue
> >> >> >>>> of
> >> >> >>>> my
> >> >> >>>> peptide I've obtain
> >> >> >>>>
> >> >> >>>> Error: unable to load fragment ''.
> >> >> >>>>
> >> >> >>>> So how I should define dirr from wich those caps groups will be
> >> >> >>>> loaded?
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Joel,
> >> >> >>>>
> >> >> >>>> I could not find such buiilder button :o
> >> >> >>>>
> >> >> >>>> when I've tried to select individual atoms from my FOR residue (
> >> >> >>>> from
> >> >> >>>> sequence panell), the overal residue with all atoms was selected
> >> >> >>>> instead
> >> >> >>>> :o
> >> >> >>>>
> >> >> >>>> James
> >> >> >>>>
> >> >> >>>> 2011/11/11 Joel Tyndall <***@otago.ac.nz>
> >> >> >>>>
> >> >> >>>> Hi James,
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> If I am correct in reading what you want you wish to change the
> >> >> >>>> FOR
> >> >> >>>> group
> >> >> >>>> to an ACE.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> I am using a PC version 1.3. Click on the builder button (right
> >> >> >>>> hand
> >> >> >>>> side
> >> >> >>>> of grey GUI)
> >> >> >>>>
> >> >> >>>> Make sure you are in Mouse mode: 3 button editing.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Click on the carbon of the FOR group and also the oxygen ( a
> white
> >> >> >>>> ball
> >> >> >>>> will appear on each atom)
> >> >> >>>>
> >> >> >>>> Then in the GUI click on the || icon adjacent to “bonds create”.
> >> >> >>>> This
> >> >> >>>> will
> >> >> >>>> give you the carbonyl.
> >> >> >>>>
> >> >> >>>> Now click on the hydrogen attached to the carbonyl carbon and
> then
> >> >> >>>> click
> >> >> >>>> in the GUI, the carbon atom C.
> >> >> >>>>
> >> >> >>>> This has now created your Acetylated nitrogen.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Then save molecule as: and you can edit the text file to change
> >> >> >>>> For
> >> >> >>>> to
> >> >> >>>> ACE.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Given this is some sort of dimer, I have just noticed that the
> >> >> >>>> second
> >> >> >>>> chain will overlap with the first.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Hope this helps
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Joel
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> From: James Starlight [mailto:***@gmail.com]
> >> >> >>>> Sent: Friday, 11 November 2011 1:44 a.m.
> >> >> >>>> To: pymol-***@lists.sourceforge.net
> >> >> >>>> Subject: [PyMOL] Editing of the pdb structure
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Dear PyMol Users!
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Recently I've opened such topic but I didnt obtain answer on
> this
> >> >> >>>> question
> >> >> >>>> so I try to paraphrase my task. Also I want to specify this
> topic
> >> >> >>>> on
> >> >> >>>> questions lincked with the processing of pdbs.
> >> >> >>>>
> >> >> >>>> 1) I need to remove some elements fron my structure described as
> >> >> >>>> the
> >> >> >>>> individual residue and place another element of the same size on
> >> >> >>>> the
> >> >> >>>> place
> >> >> >>>> of the first element.
> >> >> >>>>
> >> >> >>>> In particular I have two different peptides both of wich have
> >> >> >>>> small
> >> >> >>>> cap
> >> >> >>>> groups on C and N termi. ( attached)
> >> >> >>>>
> >> >> >>>> I need to remove all caps ( two caps FOR and ETA because there
> are
> >> >> >>>> two
> >> >> >>>> identical chains in that structure) from the 1MAG structure and
> >> >> >>>> build
> >> >> >>>> exactly on this place another cap groups wich I'd like to copy
> >> >> >>>> from
> >> >> >>>> the
> >> >> >>>> second peptide ( KALP). So I'd like to change FOR- > ACE and
> ETA->
> >> >> >>>> NH2
> >> >> >>>> twisely for the 1MAG dtructure
> >> >> >>>>
> >> >> >>>> How I can perform such task in PyMol?
> >> >> >>>>
> >> >> >>>> James
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>
> >> >> >>>
> >> >> >>>
> >> >> >>>
> ------------------------------------------------------------------------------
> >> >> >>> All the data continuously generated in your IT infrastructure
> >> >> >>> contains a definitive record of customers, application
> performance,
> >> >> >>> security threats, fraudulent activity, and more. Splunk takes
> this
> >> >> >>> data and makes sense of it. IT sense. And common sense.
> >> >> >>> http://p.sf.net/sfu/splunk-novd2d
> >> >> >>> _______________________________________________
> >> >> >>> PyMOL-users mailing list (PyMOL-***@lists.sourceforge.net)
> >> >> >>> Info Page:
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> >> >>> Archives:
> >> >> >>> http://www.mail-archive.com/pymol-***@lists.sourceforge.net
> >> >> >>>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Jason Vertrees, PhD
> >> >> >> PyMOL Product Manager
> >> >> >> Schrodinger, LLC
> >> >> >>
> >> >> >> (e) ***@schrodinger.com
> >> >> >> (o) [phone]
> >> >> >>
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Jason Vertrees, PhD
> >> >> PyMOL Product Manager
> >> >> Schrodinger, LLC
> >> >>
> >> >> (e) ***@schrodinger.com
> >> >> (o) [phone]
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Jason Vertrees, PhD
> >> PyMOL Product Manager
> >> Schrodinger, LLC
> >>
> >> (e) ***@schrodinger.com
> >> (o) [phone]
> >
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) ***@schrodinger.com
> (o) [phone]
>

[lina]

On Tuesday 10,January,2012 09:43 PM, James Starlight wrote:
> Deal all!
>
> I'm intresting about representation of the polarr contacts between
> ligand and protein
>
> 1) Usually I'm ussing Present-> Ligand sites option for that purposes
> but in my current case I'm working with GFP where tree residues form
> chromofore group of that protein.
>
> So I want to assign that three residues as the ligand and finally find
> polar contacts between that chromophore and surrounding polar residues.
> How I could do this assignment?
>
> 2) Also I'm looking in possible way to represent Names of residues wich
> forrm my ligand binding pocket. Always I represent names of residues via
> Label option. But if I choose Label -> res.names all names will be
> represented but i want to represent only the names of residues wich form
> polar contact with ligand.
>
> James


Sorry a bit off-list-topic.

the Ligplot+ can do this pretty well.

http://www.ebi.ac.uk/thornton-srv/software/LigPlus/

[James Starlight]

Dear PyMol users!

I need to create NEW covalent bond between two adjacent atoms. How this
could be done in PyMOl?

James

[Thomas Holder]

On 01/27/2012 09:11 AM, James Starlight wrote:
> Dear PyMol users!
>
> I need to create NEW covalent bond between two adjacent atoms. How this
> could be done in PyMOl?

you could have guessed it: http://pymolwiki.org/index.php/Bond
:-)

The atoms must both be within the same object.

Cheers,
Thomas

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

[James Starlight]

Arne, Thomas

Thanks alot. Bond works finw


I'd like just to ask what about geometry optimisation of the new structure

E.g I want create 5memb imidazole ring where the 2 adj atoms are apart from
1.5 A from each other.

When I've create new bond by bond command new ring look like 6memb ( like
benzol) because of long distance between adj atoms.

How I could optimise geometry of the new mollecule? Have pymol some
built-in functions like conformational search be means of monte carlo or
energy minimisation ?


James

2012/1/27 Thomas Holder <***@users.sourceforge.net>

> On 01/27/2012 09:11 AM, James Starlight wrote:
>
>> Dear PyMol users!
>>
>> I need to create NEW covalent bond between two adjacent atoms. How this
>> could be done in PyMOl?
>>
>
> you could have guessed it: http://pymolwiki.org/index.**php/Bond<http://pymolwiki.org/index.php/Bond>
> :-)
>
> The atoms must both be within the same object.
>
>
> Cheers,
> Thomas
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>

[João Rodrigues]

Dear James,

As someone has told you already, Pymol is a visualization tool, not a
modelling suite. I guess you would be better off using something like
AMBERTOOLS or MODELLER, depending on what you want to model, or any other
"real" simulation/modelling package otherwise your results are very weak...

My opinion only.

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



No dia 27 de Janeiro de 2012 09:50, James Starlight
<***@gmail.com>escreveu:

> Arne, Thomas
>
> Thanks alot. Bond works finw
>
>
> I'd like just to ask what about geometry optimisation of the new structure
>
> E.g I want create 5memb imidazole ring where the 2 adj atoms are apart
> from 1.5 A from each other.
>
> When I've create new bond by bond command new ring look like 6memb ( like
> benzol) because of long distance between adj atoms.
>
> How I could optimise geometry of the new mollecule? Have pymol some
> built-in functions like conformational search be means of monte carlo or
> energy minimisation ?
>
>
> James
>
>
> 2012/1/27 Thomas Holder <***@users.sourceforge.net>
>
>> On 01/27/2012 09:11 AM, James Starlight wrote:
>>
>>> Dear PyMol users!
>>>
>>> I need to create NEW covalent bond between two adjacent atoms. How this
>>> could be done in PyMOl?
>>>
>>
>> you could have guessed it: http://pymolwiki.org/index.**php/Bond<http://pymolwiki.org/index.php/Bond>
>> :-)
>>
>> The atoms must both be within the same object.
>>
>>
>> Cheers,
>> Thomas
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 TÃŒbingen
>>
>
>
>
> ------------------------------------------------------------------------------
> Try before you buy = See our experts in action!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-dev2
> _______________________________________________
> PyMOL-users mailing list (PyMOL-***@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-***@lists.sourceforge.net
>

[Tim Schulte]

Dear James,
I agree with Joao, for fast and dirty minimisation you might try the program Chimera or VegaZZ. If you just wanna have an energy-minimized small molecule the Prodrg server is the way to go.
Cheers,
Tim
________________________________
Von: João Rodrigues [***@gmail.com]
Gesendet: Freitag, 27. Januar 2012 09:56
Bis: James Starlight
Cc: pymol-***@lists.sourceforge.net
Betreff: Re: [PyMOL] Editing of the pdb structure

Dear James,

As someone has told you already, Pymol is a visualization tool, not a modelling suite. I guess you would be better off using something like AMBERTOOLS or MODELLER, depending on what you want to model, or any other "real" simulation/modelling package otherwise your results are very weak...

My opinion only.

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



No dia 27 de Janeiro de 2012 09:50, James Starlight <***@gmail.com<mailto:***@gmail.com>> escreveu:
Arne, Thomas

Thanks alot. Bond works finw


I'd like just to ask what about geometry optimisation of the new structure

E.g I want create 5memb imidazole ring where the 2 adj atoms are apart from 1.5 A from each other.

When I've create new bond by bond command new ring look like 6memb ( like benzol) because of long distance between adj atoms.

How I could optimise geometry of the new mollecule? Have pymol some built-in functions like conformational search be means of monte carlo or energy minimisation ?


James


2012/1/27 Thomas Holder <***@users.sourceforge.net<mailto:***@users.sourceforge.net>>
On 01/27/2012 09:11 AM, James Starlight wrote:
Dear PyMol users!

I need to create NEW covalent bond between two adjacent atoms. How this
could be done in PyMOl?

you could have guessed it: http://pymolwiki.org/index.php/Bond
:-)

The atoms must both be within the same object.


Cheers,
Thomas

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen


------------------------------------------------------------------------------
Try before you buy = See our experts in action!
The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
http://p.sf.net/sfu/learndevnow-dev2
_______________________________________________
PyMOL-users mailing list (PyMOL-***@lists.sourceforge.net<mailto:PyMOL-***@lists.sourceforge.net>)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-***@lists.sourceforge.net

[Thomas Evangelidis]

[Thomas Evangelidis]

[unknown]

--0050450176bbb35ef404b7bbd00a
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Is it a small organic molecule or a modified amino acid within the context
of a protein?


2012/1/29 Tim Schulte <***@ki.se>

> Dear James,
> I agree with Joao, for fast and dirty minimisation you might try the
> program Chimera or VegaZZ. If you just wanna have an energy-minimized small
> molecule the Prodrg server is the way to go.
> Cheers,
> Tim
> ------------------------------
> *Von:* João Rodrigues [***@gmail.com]
> *Gesendet:* Freitag, 27. Januar 2012 09:56
> *Bis:* James Starlight
> *Cc:* pymol-***@lists.sourceforge.net
> *Betreff:* Re: [PyMOL] Editing of the pdb structure
>
> Dear James,
>
> As someone has told you already, Pymol is a visualization tool, not a
> modelling suite. I guess you would be better off using something like
> AMBERTOOLS or MODELLER, depending on what you want to model, or any other
> "real" simulation/modelling package otherwise your results are very weak...
>
> My opinion only.
>
> João [...] Rodrigues
> http://nmr.chem.uu.nl/~joao
>
>
>
> No dia 27 de Janeiro de 2012 09:50, James Starlight <
> ***@gmail.com> escreveu:
>
>> Arne, Thomas
>>
>> Thanks alot. Bond works finw
>>
>>
>> I'd like just to ask what about geometry optimisation of the new structure
>>
>> E.g I want create 5memb imidazole ring where the 2 adj atoms are apart
>> from 1.5 A from each other.
>>
>> When I've create new bond by bond command new ring look like 6memb ( like
>> benzol) because of long distance between adj atoms.
>>
>> How I could optimise geometry of the new mollecule? Have pymol some
>> built-in functions like conformational search be means of monte carlo or
>> energy minimisation ?
>>
>>
>> James
>>
>>
>> 2012/1/27 Thomas Holder <***@users.sourceforge.net>
>>
>>> On 01/27/2012 09:11 AM, James Starlight wrote:
>>>
>>>> Dear PyMol users!
>>>>
>>>> I need to create NEW covalent bond between two adjacent atoms. How this
>>>> could be done in PyMOl?
>>>>
>>>
>>> you could have guessed it: http://pymolwiki.org/index.**php/Bond<http://pymolwiki.org/index.php/Bond>
>>> :-)
>>>
>>> The atoms must both be within the same object.
>>>
>>>
>>> Cheers,
>>> Thomas
>>>
>>> --
>>> Thomas Holder
>>> MPI for Developmental Biology
>>> Spemannstr. 35
>>> D-72076 Tübingen
>>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Try before you buy = See our experts in action!
>> The most comprehensive online learning library for Microsoft developers
>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>> Metro Style Apps, more. Free future releases when you subscribe now!
>> http://p.sf.net/sfu/learndevnow-dev2
>> _______________________________________________
>> PyMOL-users mailing list (PyMOL-***@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-***@lists.sourceforge.net
>>
>
>
>
> ------------------------------------------------------------------------------
> Try before you buy = See our experts in action!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-dev2
> _______________________________________________
> PyMOL-users mailing list (PyMOL-***@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-***@lists.sourceforge.net
>



--

======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: ***@bioacademy.gr

***@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/

--0050450176bbb35ef404b7bbd00a
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Is it a small organic molecule or a modified amino acid within the context of a protein?<br><br><br><div class="gmail_quote">2012/1/29 Tim Schulte <span dir="ltr">&lt;<a href="mailto:***@ki.se">***@ki.se</a>&gt;</span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">




<div>
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">Dear James,<br>
I agree with Joao, for fast and dirty minimisation you might try the program Chimera or VegaZZ. If you just wanna have an energy-minimized small molecule the Prodrg server is the way to go.<br>
Cheers,<br>
Tim<br>
<div style="font-family:Times New Roman;color:rgb(0,0,0);font-size:16px">
<hr>
<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>Von:</b> João Rodrigues [<a href="mailto:***@gmail.com" target="_blank">***@gmail.com</a>]<br>
<b>Gesendet:</b> Freitag, 27. Januar 2012 09:56<br>
<b>Bis:</b> James Starlight<br>
<b>Cc:</b> <a href="mailto:pymol-***@lists.sourceforge.net" target="_blank">pymol-***@lists.sourceforge.net</a><br>
<b>Betreff:</b> Re: [PyMOL] Editing of the pdb structure<br>
</font><br>
</div><div><div></div><div class="h5">
<div></div>
<div>Dear James,
<div><br>
</div>
<div>As someone has told you already, Pymol is a visualization tool, not a modelling suite. I guess you would be better off using something like AMBERTOOLS or MODELLER, depending on what you want to model, or any other &quot;real&quot; simulation/modelling package otherwise
your results are very weak...</div>
<div><br>
</div>
<div>My opinion only.</div>
<div><br clear="all">
João [...] Rodrigues<br>
<a href="http://nmr.chem.uu.nl/%7Ejoao" target="_blank">http://nmr.chem.uu.nl/~joao</a><br>
<br>
<br>
<br>
<div class="gmail_quote">No dia 27 de Janeiro de 2012 09:50, James Starlight <span dir="ltr">
&lt;<a href="mailto:***@gmail.com" target="_blank">***@gmail.com</a>&gt;</span> escreveu:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Arne, Thomas<br>
<br>
Thanks alot. Bond works finw<br>
<br>
<br>
I&#39;d like just to ask what about geometry optimisation of the new structure<br>
<br>
E.g I want create 5memb imidazole ring where the 2 adj atoms are apart from 1.5 A from each other.<br>
<br>
When I&#39;ve create new bond by bond command new ring look like 6memb ( like benzol) because of long distance between adj atoms.
<br>
<br>
How I could optimise geometry of the new mollecule? Have pymol some built-in functions like conformational search be means of monte carlo or energy minimisation ?<span><font color="#888888"><br>
<br>
<br>
James</font></span>
<div>
<div><br>
<br>
<div class="gmail_quote">2012/1/27 Thomas Holder <span dir="ltr">&lt;<a href="mailto:***@users.sourceforge.net" target="_blank">***@users.sourceforge.net</a>&gt;</span><br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div>On 01/27/2012 09:11 AM, James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Dear PyMol users!<br>
<br>
I need to create NEW covalent bond between two adjacent atoms. How this<br>
could be done in PyMOl?<br>
</blockquote>
<br>
</div>
</div>
you could have guessed it: <a href="http://pymolwiki.org/index.php/Bond" target="_blank">
http://pymolwiki.org/index.<u></u>php/Bond</a><br>
:-)<br>
<br>
The atoms must both be within the same object.
<div>
<div><br>
<br>
Cheers,<br>
 Thomas<br>
<br>
-- <br>
Thomas Holder<br>
MPI for Developmental Biology<br>
Spemannstr. 35<br>
D-72076 Tübingen<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
<br>
------------------------------------------------------------------------------<br>
Try before you buy = See our experts in action!<br>
The most comprehensive online learning library for Microsoft developers<br>
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,<br>
Metro Style Apps, more. Free future releases when you subscribe now!<br>
<a href="http://p.sf.net/sfu/learndevnow-dev2" target="_blank">http://p.sf.net/sfu/learndevnow-dev2</a><br>
_______________________________________________<br>
PyMOL-users mailing list (<a href="mailto:PyMOL-***@lists.sourceforge.net" target="_blank">PyMOL-***@lists.sourceforge.net</a>)<br>
Info Page: <a href="https://lists.sourceforge.net/lists/listinfo/pymol-users" target="_blank">
https://lists.sourceforge.net/lists/listinfo/pymol-users</a><br>
Archives: <a href="http://www.mail-archive.com/pymol-***@lists.sourceforge.net" target="_blank">
http://www.mail-archive.com/pymol-***@lists.sourceforge.net</a><br>
</blockquote>
</div>
<br>
</div>
</div>
</div></div></div>
</div>
</div>

<br>------------------------------------------------------------------------------<br>
Try before you buy = See our experts in action!<br>
The most comprehensive online learning library for Microsoft developers<br>
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,<br>
Metro Style Apps, more. Free future releases when you subscribe now!<br>
<a href="http://p.sf.net/sfu/learndevnow-dev2" target="_blank">http://p.sf.net/sfu/learndevnow-dev2</a><br>_______________________________________________<br>
PyMOL-users mailing list (<a href="mailto:PyMOL-***@lists.sourceforge.net">PyMOL-***@lists.sourceforge.net</a>)<br>
Info Page: <a href="https://lists.sourceforge.net/lists/listinfo/pymol-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/pymol-users</a><br>
Archives: <a href="http://www.mail-archive.com/pymol-***@lists.sourceforge.net" target="_blank">http://www.mail-archive.com/pymol-***@lists.sourceforge.net</a><br></blockquote></div><br><br clear="all"><br>-- <br>







<p style="margin-bottom:0cm" align="LEFT">======================================================================</p>
<p style="margin-bottom:0cm" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom:0cm" align="LEFT">PhD student</p>
<p style="margin-bottom:0cm" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom:0cm" align="LEFT">4 Soranou Ephessiou , 115 27
Athens, Greece<br><br>email: <a href="mailto:***@bioacademy.gr" target="_blank">***@bioacademy.gr</a></p>
<p style="margin-bottom:0cm" align="LEFT">          <a href="mailto:***@gmail.com" target="_blank">***@gmail.com</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>
</p>
<br>

--0050450176bbb35ef404b7bbd00a--

[unknown]

--20cf303f6d8439d67104b7c26656
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

I think you got your answers from the AMBER and GROMACS mailing list :)

Just a comment about PRODRG server, it is not the best choice for geometry
optimization and charge calculation.

Lemkul, J.A., Allen, W.J., and Bevan, D.R. (2010) Practical Considerations
for Building GROMOS-Compatible Small Molecule Topologies. *J. Chem. Inf.
Model.* *50* (12): 2221-2235.

To our experience in the group it tends to define the "charge groups"
inaccurately and produce optimized geometries that have out of plane
hydrogens. There is a new online service for creating GROMOS compatible
topologies for organic compounds:

http://compbio.biosci.uq.edu.au/atb/

It uses a knowledge-based approach and higher level QM calculations for
geometry optimization and charge derivation. Yet the GROMOS ffs are united
atom thus you lose in resolution.

If I had to chose an all-atom ff I would go for the AMBER99SB-ILDN for the
protein and GAFF for the organic compound (your chromophore). Unless you
have problems with the size of the organic molecule, you could optimize its
geometry and calculate RESP charges using the R.E.D. server:

http://q4md-forcefieldtools.org/REDS/

Also check out the option "Use RED IV for automatically generating amino
acid fragments " since your chromophore is covalently bonded to the protein
(I never used it so I am not sure if this will do your job).


Thomas



On 30 January 2012 14:16, James Starlight <***@gmail.com> wrote:

> Thomas,
>
> It's a big protein with the some non-standart functional group like GFP
>
> So the servers like PRORG are not good for that because of big size of the
> protein and subsiquent integration of both fragments.
>
> James
>
>
> 2012/1/30 Thomas Evangelidis <***@gmail.com>
>
>> Is it a small organic molecule or a modified amino acid within the
>> context of a protein?
>>
>>
>>
>> 2012/1/29 Tim Schulte <***@ki.se>
>>
>>> Dear James,
>>> I agree with Joao, for fast and dirty minimisation you might try the
>>> program Chimera or VegaZZ. If you just wanna have an energy-minimized small
>>> molecule the Prodrg server is the way to go.
>>> Cheers,
>>> Tim
>>> ------------------------------
>>> *Von:* João Rodrigues [***@gmail.com]
>>> *Gesendet:* Freitag, 27. Januar 2012 09:56
>>> *Bis:* James Starlight
>>> *Cc:* pymol-***@lists.sourceforge.net
>>> *Betreff:* Re: [PyMOL] Editing of the pdb structure
>>>
>>> Dear James,
>>>
>>> As someone has told you already, Pymol is a visualization tool, not a
>>> modelling suite. I guess you would be better off using something like
>>> AMBERTOOLS or MODELLER, depending on what you want to model, or any other
>>> "real" simulation/modelling package otherwise your results are very weak...
>>>
>>> My opinion only.
>>>
>>> João [...] Rodrigues
>>> http://nmr.chem.uu.nl/~joao
>>>
>>>
>>>
>>> No dia 27 de Janeiro de 2012 09:50, James Starlight <
>>> ***@gmail.com> escreveu:
>>>
>>>> Arne, Thomas
>>>>
>>>> Thanks alot. Bond works finw
>>>>
>>>>
>>>> I'd like just to ask what about geometry optimisation of the new
>>>> structure
>>>>
>>>> E.g I want create 5memb imidazole ring where the 2 adj atoms are apart
>>>> from 1.5 A from each other.
>>>>
>>>> When I've create new bond by bond command new ring look like 6memb (
>>>> like benzol) because of long distance between adj atoms.
>>>>
>>>> How I could optimise geometry of the new mollecule? Have pymol some
>>>> built-in functions like conformational search be means of monte carlo or
>>>> energy minimisation ?
>>>>
>>>>
>>>> James
>>>>
>>>>
>>>> 2012/1/27 Thomas Holder <***@users.sourceforge.net>
>>>>
>>>>> On 01/27/2012 09:11 AM, James Starlight wrote:
>>>>>
>>>>>> Dear PyMol users!
>>>>>>
>>>>>> I need to create NEW covalent bond between two adjacent atoms. How
>>>>>> this
>>>>>> could be done in PyMOl?
>>>>>>
>>>>>
>>>>> you could have guessed it: http://pymolwiki.org/index.**php/Bond<http://pymolwiki.org/index.php/Bond>
>>>>> :-)
>>>>>
>>>>> The atoms must both be within the same object.
>>>>>
>>>>>
>>>>> Cheers,
>>>>> Thomas
>>>>>
>>>>> --
>>>>> Thomas Holder
>>>>> MPI for Developmental Biology
>>>>> Spemannstr. 35
>>>>> D-72076 Tübingen
>>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Try before you buy = See our experts in action!
>>>> The most comprehensive online learning library for Microsoft developers
>>>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>>>> Metro Style Apps, more. Free future releases when you subscribe now!
>>>> http://p.sf.net/sfu/learndevnow-dev2
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyMOL-***@lists.sourceforge.net)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>> Archives: http://www.mail-archive.com/pymol-***@lists.sourceforge.net
>>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Try before you buy = See our experts in action!
>>> The most comprehensive online learning library for Microsoft developers
>>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>>> Metro Style Apps, more. Free future releases when you subscribe now!
>>> http://p.sf.net/sfu/learndevnow-dev2
>>> _______________________________________________
>>> PyMOL-users mailing list (PyMOL-***@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-***@lists.sourceforge.net
>>>
>>
>>
>>
>> --
>>
>> ======================================================================
>>
>> Thomas Evangelidis
>>
>> PhD student
>>
>> Biomedical Research Foundation, Academy of Athens
>>
>> 4 Soranou Ephessiou , 115 27 Athens, Greece
>>
>> email: ***@bioacademy.gr
>>
>> ***@gmail.com
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Try before you buy = See our experts in action!
>> The most comprehensive online learning library for Microsoft developers
>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>> Metro Style Apps, more. Free future releases when you subscribe now!
>> http://p.sf.net/sfu/learndevnow-dev2
>> _______________________________________________
>> PyMOL-users mailing list (PyMOL-***@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-***@lists.sourceforge.net
>>
>
>


--

======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: ***@bioacademy.gr

***@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/

--20cf303f6d8439d67104b7c26656
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

I think you got your answers from the AMBER and GROMACS mailing list :)<br><br>Just a comment about PRODRG server, it is not the best choice for geometry optimization and charge calculation.<br><br><font face="Arial"><font size="-1"><font size="-1">Lemkul,
J.A., Allen, W.J., and Bevan, D.R. (2010) Practical Considerations for
Building GROMOS-Compatible Small Molecule Topologies. <i>J. Chem. Inf. Model.</i> <b>50</b> (12): 2221-2235.</font></font></font><br><br>To our experience in the group it tends to define the &quot;charge groups&quot; inaccurately and produce optimized geometries that have out of plane hydrogens. There is a new online service for creating GROMOS compatible topologies for organic compounds:<br>
<br><a href="http://compbio.biosci.uq.edu.au/atb/">http://compbio.biosci.uq.edu.au/atb/</a><br><br>It uses a knowledge-based approach and higher level QM calculations for geometry optimization and charge derivation. Yet the GROMOS ffs are united atom thus you lose in resolution. <br>
<br>If I had to chose an all-atom ff I would go for the AMBER99SB-ILDN for the protein and GAFF for the organic compound (your chromophore). Unless you have problems with the size of the organic molecule, you could optimize its geometry and calculate RESP charges using the R.E.D. server:<br>
<br><a href="http://q4md-forcefieldtools.org/REDS/">http://q4md-forcefieldtools.org/REDS/</a><br><br>Also check out the option &quot;<font color="black">Use RED IV for automatically generating <a>amino acid fragments</a> &quot; since your chromophore is covalently bonded to the protein (I never used it so I am not sure if this will do your job).<br>
<br><br>Thomas<br><br></font><br><br><div class="gmail_quote">On 30 January 2012 14:16, James Starlight <span dir="ltr">&lt;<a href="mailto:***@gmail.com">***@gmail.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thomas,<br><br>It&#39;s a big protein with the some non-standart functional group like GFP<br><br>So the servers like PRORG are not good for that because of big size of the protein and subsiquent integration of both fragments.<br>
<font color="#888888">
<br>James</font><div><div></div><div class="h5"><br><br><div class="gmail_quote">2012/1/30 Thomas Evangelidis <span dir="ltr">&lt;<a href="mailto:***@gmail.com" target="_blank">***@gmail.com</a>&gt;</span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

Is it a small organic molecule or a modified amino acid within the context of a protein?<div><div><br><br><br><div class="gmail_quote">2012/1/29 Tim Schulte <span dir="ltr">&lt;<a href="mailto:***@ki.se" target="_blank">***@ki.se</a>&gt;</span><br>


<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">




<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Dear James,<br>
I agree with Joao, for fast and dirty minimisation you might try the program Chimera or VegaZZ. If you just wanna have an energy-minimized small molecule the Prodrg server is the way to go.<br>
Cheers,<br>
Tim<br>
<div style="font-size:16px;font-family:Times New Roman">
<hr>
<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>Von:</b> João Rodrigues [<a href="mailto:***@gmail.com" target="_blank">***@gmail.com</a>]<br>
<b>Gesendet:</b> Freitag, 27. Januar 2012 09:56<br>
<b>Bis:</b> James Starlight<br>
<b>Cc:</b> <a href="mailto:pymol-***@lists.sourceforge.net" target="_blank">pymol-***@lists.sourceforge.net</a><br>
<b>Betreff:</b> Re: [PyMOL] Editing of the pdb structure<br>
</font><br>
</div><div><div></div><div>
<div></div>
<div>Dear James,
<div><br>
</div>
<div>As someone has told you already, Pymol is a visualization tool, not a modelling suite. I guess you would be better off using something like AMBERTOOLS or MODELLER, depending on what you want to model, or any other &quot;real&quot; simulation/modelling package otherwise
your results are very weak...</div>
<div><br>
</div>
<div>My opinion only.</div>
<div><br clear="all">
João [...] Rodrigues<br>
<a href="http://nmr.chem.uu.nl/%7Ejoao" target="_blank">http://nmr.chem.uu.nl/~joao</a><br>
<br>
<br>
<br>
<div class="gmail_quote">No dia 27 de Janeiro de 2012 09:50, James Starlight <span dir="ltr">
&lt;<a href="mailto:***@gmail.com" target="_blank">***@gmail.com</a>&gt;</span> escreveu:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Arne, Thomas<br>
<br>
Thanks alot. Bond works finw<br>
<br>
<br>
I&#39;d like just to ask what about geometry optimisation of the new structure<br>
<br>
E.g I want create 5memb imidazole ring where the 2 adj atoms are apart from 1.5 A from each other.<br>
<br>
When I&#39;ve create new bond by bond command new ring look like 6memb ( like benzol) because of long distance between adj atoms.
<br>
<br>
How I could optimise geometry of the new mollecule? Have pymol some built-in functions like conformational search be means of monte carlo or energy minimisation ?<span><font color="#888888"><br>
<br>
<br>
James</font></span>
<div>
<div><br>
<br>
<div class="gmail_quote">2012/1/27 Thomas Holder <span dir="ltr">&lt;<a href="mailto:***@users.sourceforge.net" target="_blank">***@users.sourceforge.net</a>&gt;</span><br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div>On 01/27/2012 09:11 AM, James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Dear PyMol users!<br>
<br>
I need to create NEW covalent bond between two adjacent atoms. How this<br>
could be done in PyMOl?<br>
</blockquote>
<br>
</div>
</div>
you could have guessed it: <a href="http://pymolwiki.org/index.php/Bond" target="_blank">
http://pymolwiki.org/index.<u></u>php/Bond</a><br>
:-)<br>
<br>
The atoms must both be within the same object.
<div>
<div><br>
<br>
Cheers,<br>
 Thomas<br>
<br>
-- <br>
Thomas Holder<br>
MPI for Developmental Biology<br>
Spemannstr. 35<br>
D-72076 Tübingen<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
<br>
------------------------------------------------------------------------------<br>
Try before you buy = See our experts in action!<br>
The most comprehensive online learning library for Microsoft developers<br>
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,<br>
Metro Style Apps, more. Free future releases when you subscribe now!<br>
<a href="http://p.sf.net/sfu/learndevnow-dev2" target="_blank">http://p.sf.net/sfu/learndevnow-dev2</a><br>
_______________________________________________<br>
PyMOL-users mailing list (<a href="mailto:PyMOL-***@lists.sourceforge.net" target="_blank">PyMOL-***@lists.sourceforge.net</a>)<br>
Info Page: <a href="https://lists.sourceforge.net/lists/listinfo/pymol-users" target="_blank">
https://lists.sourceforge.net/lists/listinfo/pymol-users</a><br>
Archives: <a href="http://www.mail-archive.com/pymol-***@lists.sourceforge.net" target="_blank">
http://www.mail-archive.com/pymol-***@lists.sourceforge.net</a><br>
</blockquote>
</div>
<br>
</div>
</div>
</div></div></div>
</div>
</div>

<br>------------------------------------------------------------------------------<br>
Try before you buy = See our experts in action!<br>
The most comprehensive online learning library for Microsoft developers<br>
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,<br>
Metro Style Apps, more. Free future releases when you subscribe now!<br>
<a href="http://p.sf.net/sfu/learndevnow-dev2" target="_blank">http://p.sf.net/sfu/learndevnow-dev2</a><br>_______________________________________________<br>
PyMOL-users mailing list (<a href="mailto:PyMOL-***@lists.sourceforge.net" target="_blank">PyMOL-***@lists.sourceforge.net</a>)<br>
Info Page: <a href="https://lists.sourceforge.net/lists/listinfo/pymol-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/pymol-users</a><br>
Archives: <a href="http://www.mail-archive.com/pymol-***@lists.sourceforge.net" target="_blank">http://www.mail-archive.com/pymol-***@lists.sourceforge.net</a><br></blockquote></div><br><br clear="all"><br></div></div>

-- <br>







<p style="margin-bottom:0cm" align="LEFT">======================================================================</p>
<p style="margin-bottom:0cm" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom:0cm" align="LEFT">PhD student</p>
<p style="margin-bottom:0cm" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom:0cm" align="LEFT">4 Soranou Ephessiou , 115 27
Athens, Greece<br><br>email: <a href="mailto:***@bioacademy.gr" target="_blank">***@bioacademy.gr</a></p>
<p style="margin-bottom:0cm" align="LEFT">          <a href="mailto:***@gmail.com" target="_blank">***@gmail.com</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>
</p>
<br>
<br>------------------------------------------------------------------------------<br>
Try before you buy = See our experts in action!<br>
The most comprehensive online learning library for Microsoft developers<br>
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,<br>
Metro Style Apps, more. Free future releases when you subscribe now!<br>
<a href="http://p.sf.net/sfu/learndevnow-dev2" target="_blank">http://p.sf.net/sfu/learndevnow-dev2</a><br>_______________________________________________<br>
PyMOL-users mailing list (<a href="mailto:PyMOL-***@lists.sourceforge.net" target="_blank">PyMOL-***@lists.sourceforge.net</a>)<br>
Info Page: <a href="https://lists.sourceforge.net/lists/listinfo/pymol-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/pymol-users</a><br>
Archives: <a href="http://www.mail-archive.com/pymol-***@lists.sourceforge.net" target="_blank">http://www.mail-archive.com/pymol-***@lists.sourceforge.net</a><br></blockquote></div><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>







<p style="margin-bottom:0cm" align="LEFT">======================================================================</p>
<p style="margin-bottom:0cm" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom:0cm" align="LEFT">PhD student</p>
<p style="margin-bottom:0cm" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom:0cm" align="LEFT">4 Soranou Ephessiou , 115 27
Athens, Greece<br><br>email: <a href="mailto:***@bioacademy.gr" target="_blank">***@bioacademy.gr</a></p>
<p style="margin-bottom:0cm" align="LEFT">          <a href="mailto:***@gmail.com" target="_blank">***@gmail.com</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>
</p>
<br>

--20cf303f6d8439d67104b7c26656--

[James Starlight]

Dear PyMol users!


After editing of my pdb files by means of PyMol I've noticed that some of
my structures contain of wrong TER enties in the body of the pdb files. In
all cases I save my processed pdb file by the PyMol context menu bar.
Below you can find xxample of processed file with the wrong TER enty:

ATOM 1048 C GLN A 148 62.717 15.038 24.185
1.00159.20 C
ATOM 1049 O GLN A 148 62.170 16.003 24.721
1.00160.85 O
ATOM 1050 CB GLN A 148 60.966 14.990 22.391
1.00157.41 C
ATOM 1051 CG GLN A 148 60.245 14.214 21.299
1.00164.79 C
ATOM 1052 CD GLN A 148 61.187 13.683 20.234
1.00171.18 C
ATOM 1053 OE1 GLN A 148 62.378 13.993 20.230
1.00175.57 O
ATOM 1054 NE2 GLN A 148 60.654 12.880 19.321
1.00174.45 N
ATOM 1055 N PRO A 149 63.997 14.705 24.415
1.00152.79 N
ATOM 1056 CA PRO A 149 64.879 15.450 25.320
1.00137.09 C
ATOM 1057 C PRO A 149 65.073 16.892 24.868
1.00130.60 C
ATOM 1058 O PRO A 149 65.669 17.672 25.611
1.00127.66 O
ATOM 1059 CB PRO A 149 66.204 14.689 25.221
1.00136.58 C
ATOM 1060 CG PRO A 149 65.828 13.324 24.755
1.00144.26 C
ATOM 1061 CD PRO A 149 64.668 13.530 23.836
1.00151.11 C
TER 1062 PRO A 149
ATOM 1063 N GLY A 158 65.079 6.711 35.576
1.00221.82 N
ATOM 1064 CA GLY A 158 63.944 7.519 35.982
1.00219.41 C
ATOM 1065 C GLY A 158 62.683 6.698 36.169
1.00218.58 C
ATOM 1066 O GLY A 158 62.260 6.442 37.297
1.00218.85 O
ATOM 1067 N CYS A 159 62.080 6.285 35.059
1.00216.88 N
ATOM 1068 CA CYS A 159 60.855 5.496 35.100
1.00213.74 C
ATOM 1069 C CYS A 159 61.030 4.163 34.379
1.00214.80 C
ATOM 1070 O CYS A 159 60.118 3.336 34.354
1.00213.86 O
ATOM 1071 CB CYS A 159 59.694 6.277 34.481
1.00211.79 C
ATOM 1072 SG CYS A 159 59.342 7.859 35.283
1.00233.24 S
ATOM 1073 N GLY A 160 62.206 3.961 33.794
1.00216.16 N
ATOM 1074 CA GLY A 160 62.493 2.743 33.059
1.00217.18 C
ATOM 1075 C GLY A 160 61.866 2.749 31.679
1.00215.69 C
ATOM 1076 O GLY A 160 60.981 3.557 31.395
1.00214.72 O

In that example you can see the wrong string
TER 1062 PRO A 149

Some of my programs uncorrectly recognise such TER enties as the end of one
CHAIN and bigining of the another after TER. Could you tell me how I could
avoid of such TER after processing of my pdbs via PyMol ?

Thanks for help


James

[Thomas Holder]

Hi James,

set pdb_use_ter_records, 0

This will not use TER records at all.

Cheers,
Thomas

On 03/20/2012 08:07 AM, James Starlight wrote:
> Dear PyMol users!
>
> After editing of my pdb files by means of PyMol I've noticed that some
> of my structures contain of wrong TER enties in the body of the pdb
> files. In all cases I save my processed pdb file by the PyMol context
> menu bar.
> Below you can find xxample of processed file with the wrong TER enty:
>
> ATOM 1048 C GLN A 148 62.717 15.038 24.185
> 1.00159.20 C
> ATOM 1049 O GLN A 148 62.170 16.003 24.721
> 1.00160.85 O
> ATOM 1050 CB GLN A 148 60.966 14.990 22.391
> 1.00157.41 C
> ATOM 1051 CG GLN A 148 60.245 14.214 21.299
> 1.00164.79 C
> ATOM 1052 CD GLN A 148 61.187 13.683 20.234
> 1.00171.18 C
> ATOM 1053 OE1 GLN A 148 62.378 13.993 20.230
> 1.00175.57 O
> ATOM 1054 NE2 GLN A 148 60.654 12.880 19.321
> 1.00174.45 N
> ATOM 1055 N PRO A 149 63.997 14.705 24.415
> 1.00152.79 N
> ATOM 1056 CA PRO A 149 64.879 15.450 25.320
> 1.00137.09 C
> ATOM 1057 C PRO A 149 65.073 16.892 24.868
> 1.00130.60 C
> ATOM 1058 O PRO A 149 65.669 17.672 25.611
> 1.00127.66 O
> ATOM 1059 CB PRO A 149 66.204 14.689 25.221
> 1.00136.58 C
> ATOM 1060 CG PRO A 149 65.828 13.324 24.755
> 1.00144.26 C
> ATOM 1061 CD PRO A 149 64.668 13.530 23.836
> 1.00151.11 C
> TER 1062 PRO A 149
> ATOM 1063 N GLY A 158 65.079 6.711 35.576
> 1.00221.82 N
> ATOM 1064 CA GLY A 158 63.944 7.519 35.982
> 1.00219.41 C
> ATOM 1065 C GLY A 158 62.683 6.698 36.169
> 1.00218.58 C
> ATOM 1066 O GLY A 158 62.260 6.442 37.297
> 1.00218.85 O
> ATOM 1067 N CYS A 159 62.080 6.285 35.059
> 1.00216.88 N
> ATOM 1068 CA CYS A 159 60.855 5.496 35.100
> 1.00213.74 C
> ATOM 1069 C CYS A 159 61.030 4.163 34.379
> 1.00214.80 C
> ATOM 1070 O CYS A 159 60.118 3.336 34.354
> 1.00213.86 O
> ATOM 1071 CB CYS A 159 59.694 6.277 34.481
> 1.00211.79 C
> ATOM 1072 SG CYS A 159 59.342 7.859 35.283
> 1.00233.24 S
> ATOM 1073 N GLY A 160 62.206 3.961 33.794
> 1.00216.16 N
> ATOM 1074 CA GLY A 160 62.493 2.743 33.059
> 1.00217.18 C
> ATOM 1075 C GLY A 160 61.866 2.749 31.679
> 1.00215.69 C
> ATOM 1076 O GLY A 160 60.981 3.557 31.395
> 1.00214.72 O
>
> In that example you can see the wrong string
> TER 1062 PRO A 149
>
> Some of my programs uncorrectly recognise such TER enties as the end of
> one CHAIN and bigining of the another after TER. Could you tell me how I
> could avoid of such TER after processing of my pdbs via PyMol ?
>
> Thanks for help
>
>
> James

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

[Tsjerk Wassenaar]

Hi James,

In addition to Thomas' answer... What is _wrong_ about the TER
statement? Your chain is broken, indicated by the nonconsecutive
numbers. That means you have two distinct molecules, and they are
separated by a TER statement. Doesn't seem wrong. Yeah, they might be
the same chain, but having a broken chain without considering them as
separate molecules seems more wrong to me.

Cheers,

Tsjerk

On Tue, Mar 20, 2012 at 8:07 AM, James Starlight <***@gmail.com> wrote:
> Dear PyMol users!
>
>
> After editing of my pdb files by means of PyMol I've noticed that some of my
> structures contain of wrong TER enties in the body of the pdb files. In all
> cases I save my processed pdb file by the PyMol context menu bar.
> Below you can find xxample of processed file with the wrong TER enty:
>
> ATOM   1048  C   GLN A 148      62.717  15.038  24.185  1.00159.20
> C
> ATOM   1049  O   GLN A 148      62.170  16.003  24.721  1.00160.85
> O
> ATOM   1050  CB  GLN A 148      60.966  14.990  22.391  1.00157.41
> C
> ATOM   1051  CG  GLN A 148      60.245  14.214  21.299  1.00164.79
> C
> ATOM   1052  CD  GLN A 148      61.187  13.683  20.234  1.00171.18
> C
> ATOM   1053  OE1 GLN A 148      62.378  13.993  20.230  1.00175.57
> O
> ATOM   1054  NE2 GLN A 148      60.654  12.880  19.321  1.00174.45
> N
> ATOM   1055  N   PRO A 149      63.997  14.705  24.415  1.00152.79
> N
> ATOM   1056  CA  PRO A 149      64.879  15.450  25.320  1.00137.09
> C
> ATOM   1057  C   PRO A 149      65.073  16.892  24.868  1.00130.60
> C
> ATOM   1058  O   PRO A 149      65.669  17.672  25.611  1.00127.66
> O
> ATOM   1059  CB  PRO A 149      66.204  14.689  25.221  1.00136.58
> C
> ATOM   1060  CG  PRO A 149      65.828  13.324  24.755  1.00144.26
> C
> ATOM   1061  CD  PRO A 149      64.668  13.530  23.836  1.00151.11
> C
> TER    1062      PRO A 149
> ATOM   1063  N   GLY A 158      65.079   6.711  35.576  1.00221.82
> N
> ATOM   1064  CA  GLY A 158      63.944   7.519  35.982  1.00219.41
> C
> ATOM   1065  C   GLY A 158      62.683   6.698  36.169  1.00218.58
> C
> ATOM   1066  O   GLY A 158      62.260   6.442  37.297  1.00218.85
> O
> ATOM   1067  N   CYS A 159      62.080   6.285  35.059  1.00216.88
> N
> ATOM   1068  CA  CYS A 159      60.855   5.496  35.100  1.00213.74
> C
> ATOM   1069  C   CYS A 159      61.030   4.163  34.379  1.00214.80
> C
> ATOM   1070  O   CYS A 159      60.118   3.336  34.354  1.00213.86
> O
> ATOM   1071  CB  CYS A 159      59.694   6.277  34.481  1.00211.79
> C
> ATOM   1072  SG  CYS A 159      59.342   7.859  35.283  1.00233.24
> S
> ATOM   1073  N   GLY A 160      62.206   3.961  33.794  1.00216.16
> N
> ATOM   1074  CA  GLY A 160      62.493   2.743  33.059  1.00217.18
> C
> ATOM   1075  C   GLY A 160      61.866   2.749  31.679  1.00215.69
> C
> ATOM   1076  O   GLY A 160      60.981   3.557  31.395  1.00214.72
> O
>
> In that example you can see the wrong string
> TER    1062      PRO A 149
>
> Some of my programs uncorrectly recognise such TER enties as the end of one
> CHAIN and bigining of the another after TER. Could you tell me how I could
> avoid of such TER after processing of my pdbs via PyMol ?
>
> Thanks for help
>
>
> James
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> PyMOL-users mailing list (PyMOL-***@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-***@lists.sourceforge.net



--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

[Thomas Holder]

On 03/20/2012 11:35 AM, Tsjerk Wassenaar wrote:
> In addition to Thomas' answer... What is _wrong_ about the TER
> statement? Your chain is broken, indicated by the nonconsecutive
> numbers. That means you have two distinct molecules, and they are
> separated by a TER statement. Doesn't seem wrong. Yeah, they might be
> the same chain, but having a broken chain without considering them as
> separate molecules seems more wrong to me.

depends on circumstances. Many algorithms (like alignment/superposition)
work fine even with gapped chains. There are some applications which
stop reading a PDB file on the first TER record, like TMalign. So when
preparing input for TMalign with PyMOL, you most likely want to skip any
TER records.

Cheers,
Thomas

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

[Tsjerk Wassenaar]

Hi Thomas,

'Wrong', certainly in the context it was given in, is a statement of
judgment. It suggest that there is a failure in the functioning, and
is a criticism to the developer, becoming a wrongdoer. My argument is,
that the answer given (with TER statements) is not wrong, but from a
chemical and biological point of view, and in light of the PDB format,
is actually more correct. It may be inconvenient for post-processing
with some other tools, but that is easily taken care of by changing a
setting (unset use_ter_records), or by post-processing (sed -i /TER/d
file.pdb).

Cheers,

Tsjerk

On Tue, Mar 20, 2012 at 1:14 PM, Thomas Holder
<***@users.sourceforge.net> wrote:
> On 03/20/2012 11:35 AM, Tsjerk Wassenaar wrote:
>>
>> In addition to Thomas' answer... What is _wrong_ about the TER
>> statement? Your chain is broken, indicated by the nonconsecutive
>> numbers. That means you have two distinct molecules, and they are
>> separated by a TER statement. Doesn't seem wrong. Yeah, they might be
>> the same chain, but having a broken chain without considering them as
>> separate molecules seems more wrong to me.
>
>
> depends on circumstances. Many algorithms (like alignment/superposition)
> work fine even with gapped chains. There are some applications which stop
> reading a PDB file on the first TER record, like TMalign. So when preparing
> input for TMalign with PyMOL, you most likely want to skip any TER records.
>
> Cheers,
>  Thomas
>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen



--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

[Tsjerk Wassenaar]

Shucks! So much for trying to keep the developer out of the wind. But
he's a wrongdoer by PDB definitions anyway! So it would be best to
modify the behaviour concerning writing of TER records. Feel free to
file it as suggestion.

Gotta love polemics! -- Next time I'll manage, David. Next time... :p

Tsjerk

On Tue, Mar 20, 2012 at 2:48 PM, David Hall <***@cowsandmilk.net> wrote:
> On Tue, Mar 20, 2012 at 8:44 AM, Tsjerk Wassenaar <***@gmail.com> wrote:
>> Hi Thomas,
>>
>> 'Wrong', certainly in the context it was given in, is a statement of
>> judgment. It suggest that there is a failure in the functioning, and
>> is a criticism to the developer, becoming a wrongdoer. My argument is,
>> that the answer given (with TER statements) is not wrong, but from a
>> chemical and biological point of view, and in light of the PDB format,
>> is actually more correct.
>
> The PDB format says:
> The TER records occur in the coordinate section of the entry, and
> indicate the last residue presented for each polypeptide and/or
> nucleic acid chain for which there are determined coordinates. For
> proteins, the residue defined on the TER record is the
> carboxy-terminal residue; for nucleic acids it is the 3'-terminal
> residue.
> ( http://www.wwpdb.org/documentation/format33/sect9.html#TER )
>
> Chain breaks in crystal structures are generally not the
> carboxy-terminal residues.
>
> -David



--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

[David Hall]

On Tue, Mar 20, 2012 at 8:44 AM, Tsjerk Wassenaar <***@gmail.com> wrote:
> Hi Thomas,
>
> 'Wrong', certainly in the context it was given in, is a statement of
> judgment. It suggest that there is a failure in the functioning, and
> is a criticism to the developer, becoming a wrongdoer. My argument is,
> that the answer given (with TER statements) is not wrong, but from a
> chemical and biological point of view, and in light of the PDB format,
> is actually more correct.

The PDB format says:
The TER records occur in the coordinate section of the entry, and
indicate the last residue presented for each polypeptide and/or
nucleic acid chain for which there are determined coordinates. For
proteins, the residue defined on the TER record is the
carboxy-terminal residue; for nucleic acids it is the 3'-terminal
residue.
( http://www.wwpdb.org/documentation/format33/sect9.html#TER )

Chain breaks in crystal structures are generally not the
carboxy-terminal residues.

-David

[Xiaoshan Min]

Hi All,

We have different versions of Pymol (1.4 and 1.5.0.3) on different computers, mainly due to some low end intel graphic chipset not able to support 1.5 version. I would like to know if there is an option to open in pymol 1.4 the pse files that were saved in pymol 1.5.  It is generally ok to open 1.4 version .pse in Pymol 1.5, but we had problems to open 1.5 version .pse in pymol 1.4.  How can I save files in Pymol 1.5 so that they will be readable in both 1.4 and 1.5 versions.

Thanks in advance.

Xiaoshan Min
Amgen San Francisco.

[Tsjerk Wassenaar]

Hi James,

Pymol adds a TER statement at the end of each continuous piece of the protein.

Cheers,

Tsjerk

2012/3/21 James Starlight <***@gmail.com>:
> Hi Tsjerk,
>
> I'm not quite understood if pymol adds TER enty after residues wich consist
> of missing atoms or in the place with the missing residues  ( e.g in loops
> of GPCRs or other flexible regions) ?
>
> James
>
> 21 марта 2012 г. 10:38 пользователь Tsjerk Wassenaar <***@gmail.com>
> написал:
>
>> Hi James,
>>
>> Broken refers to non-continuity of a chain, i.e. missing residues. Broken
>> does not mean wrong... But for the rest, I admitted to be wrong with my
>> arguments already :p
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Mar 21, 2012 6:47 AM, "James Starlight" <***@gmail.com> wrote:
>>
>> Hi Tsjerk!
>>
>> It's very strange because I've obtained all same structures with the same
>> TER statements in the body of the pdb file in the case of processing of
>> x-ray structures of GPCRs ( It's different membrane proteins solved by the
>> different lab groups in the different time ). So it's strange that all of
>> those structures were broken!
>>
>> James
>>
>> 20 марта 2012 г. 14:35 пользователь Tsjerk Wassenaar <***@gmail.com>
>> написал:
>>
>> > > Hi James, > > In addition to Thomas' answer... What is _wrong_ about
>> > > the TER > statement? Your ...
>>
>>
>



--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

[James Starlight]

[Thomas Holder]

Hi James,

"connect_mode" is for loading. I think "pdb_conect_all" is what you are
looking for:

set pdb_conect_all

http://www.pymolwiki.org/index.php/Pdb_Conect_All
http://www.pymolwiki.org/index.php/Connect_mode

Cheers,
Thomas

James Starlight wrote, On 03/30/12 11:53:
> Hi all :)
>
> Recently I've been needed to parametrise my short protein mollecule by
> ATB server for futher MD simulation.
>
> The input pdb file for that server must consist of CONNECT records at
> the bottom of such pdb.
>
> How I could add such missing CONNECT records for my pdb ?
>
> I've tried
>
> set connect_mode, 1
>
> but saved pdb still have not contained CONNECT :(
>
> Thanks for help
>
> James

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tu"bingen

[James Starlight]

Dear PyMol users!


I have some structure.pdb from the md simulation wich consist of 1 chain
not defined in the pdb file explicitly ( missing chain id in the pdb file).
So the pymol recognise that chain as the ' ' . I need to rename this
chain to the desired name ( e.g to chain A ).

How I could do it?

James

1 апреля 2012 г. 15:04 пПльзПватель James Starlight
<***@gmail.com>МапОсал:

> Thomas,
>
>
> thank you I'll test your script with modeller after obtaining of this
> software on my workstation and post here results :)
>
>
> James
>
> 1 апреля 2012 г. 12:30 пПльзПватель Thomas Holder <
> ***@users.sourceforge.net> МапОсал:
>
> Hi James,
>>
>> I use Modeller for exactly such tasks (build missing residues). It's free
>> for academic use.
>>
>> http://salilab.org/modeller/
>>
>> Using modeller is also not "comfortable" since it only has a python
>> scripting interface and thus requires you to write a script for each task.
>> But I wrote a general purpose automodel client which is quite convenient
>> for simple modelling tasks. See attachment.
>>
>> Usage:
>> python automodeller.py sequence.fasta template.pdb
>>
>> I provide this script "as is" without any warranty :) Let me know if it
>> works for you.
>>
>> Cheers,
>> Thomas
>>
>> James Starlight wrote, On 04/01/12 08:55:
>>
>> Hi Thomas!
>>>
>>> Thanks for help- this works good :)
>>>
>>>
>>> By the way I have some question not about pymol :)
>>> I've already looked for some software for processing of my PDB
>>> structure for a long time ( often I need to build missing residues and
>>> flexible LOOP fragments with some refining of the result ). For such
>>> purposes I've used amber tools software but I've found that this tools are
>>> not very comfortable for me :)
>>>
>>> Also I've found exactly what I need for in the MAESTRO's prime module
>>> but this tools avialable for the licensing only.
>>>
>>> Is there any other free software for structure processing with
>>> easy-to-use interface and free academical ussage ?
>>>
>>> Thanks again
>>>
>>> James
>>>
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 TÃŒbingen
>>
>
>

[Thomas Holder]

Hi James,

use the alter command:

alter chain "", chain="A"

See also http://pymolwiki.org/index.php/Alter

Cheers,
Thomas

James Starlight wrote, On 04/26/12 09:18:
> Dear PyMol users!
>
>
> I have some structure.pdb from the md simulation wich consist of 1 chain
> not defined in the pdb file explicitly ( missing chain id in the pdb
> file). So the pymol recognise that chain as the ' ' . I need to rename
> this chain to the desired name ( e.g to chain A ).
>
> How I could do it?
>
> James

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

[James Starlight]

Thanks Thomas!


Another question-
I have my protein.pdb with some inserted crystall waters within protein
interiour as well as water surrounded of my protein. I want to remove only
sorrounding water but prevent internal water ( wich could be functional
relevant ).

How I could to select such surrounded water ( e.g via some cutoff radius
relative my protein etc) wich I'd like to remove further ?

26 апреля 2012 г. 11:22 пПльзПватель Thomas Holder <
***@users.sourceforge.net> МапОсал:

> Hi James,
>
> use the alter command:
>
> alter chain "", chain="A"
>
> See also http://pymolwiki.org/index.**php/Alter<http://pymolwiki.org/index.php/Alter>
>
> Cheers,
> Thomas
>
> James Starlight wrote, On 04/26/12 09:18:
>
> Dear PyMol users!
>>
>>
>> I have some structure.pdb from the md simulation wich consist of 1 chain
>> not defined in the pdb file explicitly ( missing chain id in the pdb file).
>> So the pymol recognise that chain as the ' ' . I need to rename this
>> chain to the desired name ( e.g to chain A ).
>>
>> How I could do it?
>>
>> James
>>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 TÃŒbingen
>

[James Starlight]

Dear all!

I want to prepare my pdb structure for MD simulation. I've done all
required things but my protein consist of some missing heavy atoms the list
of which I've obtained from my pdb hedader

REMARK 470 M RES CSSEQI ATOMS
REMARK 470 ARG A 220 CG CD NE CZ NH1 NH2
REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2
REMARK 470 ASN B 212 O CG OD1 ND2
REMARK 470 LYS C 43 CG CD CE NZ
REMARK 470 GLY C 225 O


I've heard that there are some web servers wich could be usefull to
build such missing atoms.
In particular in my structure there are lack not only side chain atoms
but also two backbone Oxygens in the Gly and Asn wich could be the
main problem of such task.

In any case I'll be very thankfull if you provide me with such server

James



26 апреля 2012 г. 12:55 пПльзПватель James Starlight <***@gmail.com
> МапОсал:

> Thanks Thomas!
>
>
> Another question-
> I have my protein.pdb with some inserted crystall waters within protein
> interiour as well as water surrounded of my protein. I want to remove only
> sorrounding water but prevent internal water ( wich could be functional
> relevant ).
>
> How I could to select such surrounded water ( e.g via some cutoff radius
> relative my protein etc) wich I'd like to remove further ?
>
> 26 апреля 2012 г. 11:22 пПльзПватель Thomas Holder <
> ***@users.sourceforge.net> МапОсал:
>
> Hi James,
>>
>> use the alter command:
>>
>> alter chain "", chain="A"
>>
>> See also http://pymolwiki.org/index.**php/Alter<http://pymolwiki.org/index.php/Alter>
>>
>> Cheers,
>> Thomas
>>
>> James Starlight wrote, On 04/26/12 09:18:
>>
>> Dear PyMol users!
>>>
>>>
>>> I have some structure.pdb from the md simulation wich consist of 1 chain
>>> not defined in the pdb file explicitly ( missing chain id in the pdb file).
>>> So the pymol recognise that chain as the ' ' . I need to rename this
>>> chain to the desired name ( e.g to chain A ).
>>>
>>> How I could do it?
>>>
>>> James
>>>
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 TÃŒbingen
>>
>
>

[Joel Tyndall]

Surely you could use pymol mutagenesis wizard to do tis.

Also James, It is a good practice to start a new thread (new email with new subject for each set of questions you have

Regards

Joel

From: James Starlight [mailto:***@gmail.com]
Sent: Friday, 27 April 2012 8:25 p.m.
To: pymol-users
Subject: Re: [PyMOL] Editing of the pdb structure

Dear all!

I want to prepare my pdb structure for MD simulation. I've done all required things but my protein consist of some missing heavy atoms the list of which I've obtained from my pdb hedader

REMARK 470 M RES CSSEQI ATOMS

REMARK 470 ARG A 220 CG CD NE CZ NH1 NH2

REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2

REMARK 470 ASN B 212 O CG OD1 ND2

REMARK 470 LYS C 43 CG CD CE NZ

REMARK 470 GLY C 225 O


I've heard that there are some web servers wich could be usefull to build such missing atoms.
In particular in my structure there are lack not only side chain atoms but also two backbone Oxygens in the Gly and Asn wich could be the main problem of such task.


In any case I'll be very thankfull if you provide me with such server

James

26 апреля 2012 г. 12:55 пПльзПватель James Starlight <***@gmail.com<mailto:***@gmail.com>> МапОсал:
Thanks Thomas!


Another question-
I have my protein.pdb with some inserted crystall waters within protein interiour as well as water surrounded of my protein. I want to remove only sorrounding water but prevent internal water ( wich could be functional relevant ).

How I could to select such surrounded water ( e.g via some cutoff radius relative my protein etc) wich I'd like to remove further ?
26 апреля 2012 г. 11:22 пПльзПватель Thomas Holder <***@users.sourceforge.net<mailto:***@users.sourceforge.net>> МапОсал:

Hi James,

use the alter command:

alter chain "", chain="A"

See also http://pymolwiki.org/index.php/Alter

Cheers,
Thomas

James Starlight wrote, On 04/26/12 09:18:

Dear PyMol users!


I have some structure.pdb from the md simulation wich consist of 1 chain not defined in the pdb file explicitly ( missing chain id in the pdb file). So the pymol recognise that chain as the ' ' . I need to rename this chain to the desired name ( e.g to chain A ).

How I could do it?

James

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 TÃŒbingen

[Thomas Holder]

Hi James and Joel,

I would use a homology modeling tool to add missing atoms (basically
rebuild the structure, given the incomplete structure as template).

Examples for web servers:
* http://toolkit.tuebingen.mpg.de/modeller
* http://swissmodel.expasy.org/

pdb2pqr can also add a limited number of missing atoms, see
http://www.poissonboltzmann.org/pdb2pqr/d/web-servers

Hope that helps.

Cheers,
Thomas

Joel Tyndall wrote, On 04/30/12 00:07:
> Surely you could use pymol mutagenesis wizard to do tis.
>
> Also James, It is a good practice to start a new thread (new email with
> new subject for each set of questions you have
>
> Regards
>
> Joel
>
> From: James Starlight [mailto:***@gmail.com]
> Sent: Friday, 27 April 2012 8:25 p.m.
> To: pymol-users
> Subject: Re: [PyMOL] Editing of the pdb structure
>
> Dear all!
>
> I want to prepare my pdb structure for MD simulation. I've done all
> required things but my protein consist of some missing heavy atoms the
> list of which I've obtained from my pdb hedader
>
> REMARK 470 M RES CSSEQI ATOMS
> REMARK 470 ARG A 220 CG CD NE CZ NH1 NH2
> REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2
> REMARK 470 ASN B 212 O CG OD1 ND2
> REMARK 470 LYS C 43 CG CD CE NZ
> REMARK 470 GLY C 225 O
>
> I've heard that there are some web servers wich could be usefull to build such missing atoms.
> In particular in my structure there are lack not only side chain atoms but also two backbone Oxygens in the Gly and Asn wich could be the main problem of such task.
>
> In any case I'll be very thankfull if you provide me with such server
>
> James

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

[James Starlight]

Dear all!


I have input multi state structure consisted of protein in one state
and ligand in the second state generated by Chimera. I want to merge
both of that objects in one common object. How I could do it?


James

2012/7/18 James Starlight <***@gmail.com>:
> Dear all!
>
>
> I have input multi state structure consisted of protein in one state
> and ligand in the second state generated by Chimera. I want to merge
> both of that objects in one common object. How I could do it?
>
>
> James
>
> 2012/4/30 Thomas Holder <***@users.sourceforge.net>:
>> Hi James and Joel,
>>
>> I would use a homology modeling tool to add missing atoms (basically rebuild
>> the structure, given the incomplete structure as template).
>>
>> Examples for web servers:
>> * http://toolkit.tuebingen.mpg.de/modeller
>> * http://swissmodel.expasy.org/
>>
>> pdb2pqr can also add a limited number of missing atoms, see
>> http://www.poissonboltzmann.org/pdb2pqr/d/web-servers
>>
>>
>> Hope that helps.
>>
>> Cheers,
>> Thomas
>>
>> Joel Tyndall wrote, On 04/30/12 00:07:
>>
>>> Surely you could use pymol mutagenesis wizard to do tis.
>>>
>>> Also James, It is a good practice to start a new thread (new email with
>>> new subject for each set of questions you have
>>>
>>> Regards
>>>
>>> Joel
>>>
>>> From: James Starlight [mailto:***@gmail.com]
>>> Sent: Friday, 27 April 2012 8:25 p.m.
>>> To: pymol-users
>>> Subject: Re: [PyMOL] Editing of the pdb structure
>>>
>>> Dear all!
>>>
>>> I want to prepare my pdb structure for MD simulation. I've done all
>>> required things but my protein consist of some missing heavy atoms the list
>>> of which I've obtained from my pdb hedader
>>>
>>> REMARK 470 M RES CSSEQI ATOMS
>>> REMARK 470 ARG A 220 CG CD NE CZ NH1 NH2
>>> REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2
>>> REMARK 470 ASN B 212 O CG OD1 ND2
>>> REMARK 470 LYS C 43 CG CD CE NZ
>>> REMARK 470 GLY C 225 O
>>> I've heard that there are some web servers wich could be usefull to build
>>> such missing atoms.
>>> In particular in my structure there are lack not only side chain atoms but
>>> also two backbone Oxygens in the Gly and Asn wich could be the main problem
>>> of such task.
>>>
>>> In any case I'll be very thankfull if you provide me with such server
>>> James
>>
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen

[Jason Vertrees]

James,

I can't think of a clever way at the moment, so here's a simple
solution. Just create a temporary copy of the ligand from state 2 into
state 1. Then, create the new object from the protein and new_ligand:

# create a new one-state ligand from state 2 of the original

create new_ligand, old_ligand, 1, 2

# create the new_obj from

create new_obj, (new_ligand or protein), 1, 1

The object, new_obj, will have the ligand and protein both, now, in state 1.

Alternatively, you load the multi-state structure using the multiplex
flag and use create on the new objects:

load some_file.pdb, multiplex=1

create new_obj, (some_file1 or some_file2)

Cheers,

-- Jason


On Wed, Jul 18, 2012 at 12:57 PM, James Starlight
<***@gmail.com> wrote:
> Dear all!
>
>
> I have input multi state structure consisted of protein in one state
> and ligand in the second state generated by Chimera. I want to merge
> both of that objects in one common object. How I could do it?
>
>
> James
>
> 2012/7/18 James Starlight <***@gmail.com>:
>> Dear all!
>>
>>
>> I have input multi state structure consisted of protein in one state
>> and ligand in the second state generated by Chimera. I want to merge
>> both of that objects in one common object. How I could do it?
>>
>>
>> James
>>
>> 2012/4/30 Thomas Holder <***@users.sourceforge.net>:
>>> Hi James and Joel,
>>>
>>> I would use a homology modeling tool to add missing atoms (basically rebuild
>>> the structure, given the incomplete structure as template).
>>>
>>> Examples for web servers:
>>> * http://toolkit.tuebingen.mpg.de/modeller
>>> * http://swissmodel.expasy.org/
>>>
>>> pdb2pqr can also add a limited number of missing atoms, see
>>> http://www.poissonboltzmann.org/pdb2pqr/d/web-servers
>>>
>>>
>>> Hope that helps.
>>>
>>> Cheers,
>>> Thomas
>>>
>>> Joel Tyndall wrote, On 04/30/12 00:07:
>>>
>>>> Surely you could use pymol mutagenesis wizard to do tis.
>>>>
>>>> Also James, It is a good practice to start a new thread (new email with
>>>> new subject for each set of questions you have
>>>>
>>>> Regards
>>>>
>>>> Joel
>>>>
>>>> From: James Starlight [mailto:***@gmail.com]
>>>> Sent: Friday, 27 April 2012 8:25 p.m.
>>>> To: pymol-users
>>>> Subject: Re: [PyMOL] Editing of the pdb structure
>>>>
>>>> Dear all!
>>>>
>>>> I want to prepare my pdb structure for MD simulation. I've done all
>>>> required things but my protein consist of some missing heavy atoms the list
>>>> of which I've obtained from my pdb hedader
>>>>
>>>> REMARK 470 M RES CSSEQI ATOMS
>>>> REMARK 470 ARG A 220 CG CD NE CZ NH1 NH2
>>>> REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2
>>>> REMARK 470 ASN B 212 O CG OD1 ND2
>>>> REMARK 470 LYS C 43 CG CD CE NZ
>>>> REMARK 470 GLY C 225 O
>>>> I've heard that there are some web servers wich could be usefull to build
>>>> such missing atoms.
>>>> In particular in my structure there are lack not only side chain atoms but
>>>> also two backbone Oxygens in the Gly and Asn wich could be the main problem
>>>> of such task.
>>>>
>>>> In any case I'll be very thankfull if you provide me with such server
>>>> James
>>>
>>>
>>> --
>>> Thomas Holder
>>> MPI for Developmental Biology
>>> Spemannstr. 35
>>> D-72076 Tübingen
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> PyMOL-users mailing list (PyMOL-***@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-***@lists.sourceforge.net



--
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) ***@schrodinger.com
(o) [phone]

[unknown]

--e89a8f642daaaafe0104bc72cfd7
Content-Type: text/plain; charset=KOI8-R
Content-Transfer-Encoding: quoted-printable

Hi all :)


Recently I've been needed to parametrise my short protein mollecule by ATB
server for futher MD simulation.

The input pdb file for that server must consist of CONNECT records at the
bottom of such pdb.

How I could add such missing CONNECT records for my pdb ?

I've tried

set connect_mode, 1



but saved pdb still have not contained CONNECT :(

Thanks for help

James

30 марта 2012 г. 13:52 пользователь James Starlight
<***@gmail.com>написал:

> Hi all :)
>
>
> Recently I've been needed to parametrise my short protein mollecule by ATB
> server for futher MD simulation.
>
> The input pdb file for that server must consist of CONNECT records at the
> bottom of such pdb.
>
> How I could add such missing CONNECT records for my pdb ?
>
> I've tried
>
> set connect_mode, 1
>
>
>
> but saved pdb still have not contained CONNECT :(
>
> Thanks for help
>
> James
>
> 21 марта 2012 г. 13:14 пользователь Tsjerk Wassenaar <***@gmail.com>написал:
>
> Hi James,
>>
>> Pymol adds a TER statement at the end of each continuous piece of the
>> protein.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> 2012/3/21 James Starlight <***@gmail.com>:
>> > Hi Tsjerk,
>> >
>> > I'm not quite understood if pymol adds TER enty after residues wich
>> consist
>> > of missing atoms or in the place with the missing residues ( e.g in
>> loops
>> > of GPCRs or other flexible regions) ?
>> >
>> > James
>> >
>> > 21 марта 2012 г. 10:38 пользователь Tsjerk Wassenaar <***@gmail.com
>> >
>> > написал:
>> >
>> >> Hi James,
>> >>
>> >> Broken refers to non-continuity of a chain, i.e. missing residues.
>> Broken
>> >> does not mean wrong... But for the rest, I admitted to be wrong with my
>> >> arguments already :p
>> >>
>> >> Cheers,
>> >>
>> >> Tsjerk
>> >>
>> >> On Mar 21, 2012 6:47 AM, "James Starlight" <***@gmail.com>
>> wrote:
>> >>
>> >> Hi Tsjerk!
>> >>
>> >> It's very strange because I've obtained all same structures with the
>> same
>> >> TER statements in the body of the pdb file in the case of processing of
>> >> x-ray structures of GPCRs ( It's different membrane proteins solved by
>> the
>> >> different lab groups in the different time ). So it's strange that all
>> of
>> >> those structures were broken!
>> >>
>> >> James
>> >>
>> >> 20 марта 2012 г. 14:35 пользователь Tsjerk Wassenaar <
>> ***@gmail.com>
>> >> написал:
>> >>
>> >> > > Hi James, > > In addition to Thomas' answer... What is _wrong_
>> about
>> >> > > the TER > statement? Your ...
>> >>
>> >>
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>>
>
>

--e89a8f642daaaafe0104bc72cfd7
Content-Type: text/html; charset=KOI8-R
Content-Transfer-Encoding: quoted-printable

Hi all :)<br><br><br>Recently I&#39;ve been needed to parametrise my short protein mollecule by ATB server for futher MD simulation.<br><br>The input pdb file for that server must consist of CONNECT records at the bottom of such pdb.<br>

<br>How I could add such missing CONNECT records for my pdb ?<br><br>I&#39;ve tried <br><br><pre><span>set</span> connect_mode<span>,</span> <span>1</span></pre><br><br>but saved pdb still have not contained CONNECT :(<br>

<br>Thanks for help<br><br>James <br><br><div class="gmail_quote">30 марта 2012 г. 13:52 пользователь James Starlight <span dir="ltr">&lt;<a href="mailto:***@gmail.com">***@gmail.com</a>&gt;</span> написал:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all :)<br><br><br>Recently I&#39;ve been needed to parametrise my short protein mollecule by ATB server for futher MD simulation.<br>
<br>The input pdb file for that server must consist of CONNECT records at the bottom of such pdb.<br>
<br>How I could add such missing CONNECT records for my pdb ?<br><br>I&#39;ve tried <br><br><pre><span>set</span> connect_mode<span>,</span> <span>1</span></pre><br><br>but saved pdb still have not contained CONNECT :(<br>

<br>Thanks for help<br><br>James <br><br><div class="gmail_quote">21 марта 2012 г. 13:14 пользователь Tsjerk Wassenaar <span dir="ltr">&lt;<a href="mailto:***@gmail.com" target="_blank">***@gmail.com</a>&gt;</span> написал:<div>
<div class="h5"><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi James,<br>
<br>
Pymol adds a TER statement at the end of each continuous piece of the protein.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
2012/3/21 James Starlight &lt;<a href="mailto:***@gmail.com" target="_blank">***@gmail.com</a>&gt;:<br>
<div><div>&gt; Hi Tsjerk,<br>
&gt;<br>
&gt; I&#39;m not quite understood if pymol adds TER enty after residues wich consist<br>
&gt; of missing atoms or in the place with the missing residues  ( e.g in loops<br>
&gt; of GPCRs or other flexible regions) ?<br>
&gt;<br>
&gt; James<br>
&gt;<br>
&gt; 21 марта 2012 г. 10:38 пользователь Tsjerk Wassenaar &lt;<a href="mailto:***@gmail.com" target="_blank">***@gmail.com</a>&gt;<br>
&gt; написал:<br>
&gt;<br>
&gt;&gt; Hi James,<br>
&gt;&gt;<br>
&gt;&gt; Broken refers to non-continuity of a chain, i.e. missing residues. Broken<br>
&gt;&gt; does not mean wrong... But for the rest, I admitted to be wrong with my<br>
&gt;&gt; arguments already :p<br>
&gt;&gt;<br>
&gt;&gt; Cheers,<br>
&gt;&gt;<br>
&gt;&gt; Tsjerk<br>
&gt;&gt;<br>
&gt;&gt; On Mar 21, 2012 6:47 AM, &quot;James Starlight&quot; &lt;<a href="mailto:***@gmail.com" target="_blank">***@gmail.com</a>&gt; wrote:<br>
&gt;&gt;<br>
&gt;&gt; Hi Tsjerk!<br>
&gt;&gt;<br>
&gt;&gt; It&#39;s very strange because I&#39;ve obtained all same structures with the same<br>
&gt;&gt; TER statements in the body of the pdb file in the case of processing of<br>
&gt;&gt; x-ray structures of GPCRs ( It&#39;s different membrane proteins solved by the<br>
&gt;&gt; different lab groups in the different time ). So it&#39;s strange that all of<br>
&gt;&gt; those structures were broken!<br>
&gt;&gt;<br>
&gt;&gt; James<br>
&gt;&gt;<br>
&gt;&gt; 20 марта 2012 г. 14:35 пользователь Tsjerk Wassenaar &lt;<a href="mailto:***@gmail.com" target="_blank">***@gmail.com</a>&gt;<br>
&gt;&gt; написал:<br>
&gt;&gt;<br>
&gt;&gt; &gt; &gt; Hi James, &gt; &gt; In addition to Thomas&#39; answer... What is _wrong_ about<br>
&gt;&gt; &gt; &gt; the TER &gt; statement? Your ...<br>
&gt;&gt;<br>
&gt;&gt;<br>
&gt;<br>
<br>
<br>
<br>
</div></div><div><div>--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
</div></div></blockquote></div></div></div><br>
</blockquote></div><br>

--e89a8f642daaaafe0104bc72cfd7--