[PyMOL] Different color on each side of strand

Discussion:

Keitaro Yamashita

2011-03-06 15:01:08 UTC

Dear all,

Can PyMOL set different colors on each side of cartoon strand?

I tried cartoon_discrete_colors but it was not for this purpose.
(I mean the sides from which sidechains are protruded.)

Thanks in advance,

Keitaro

Jason Vertrees

2011-03-06 19:43:03 UTC

Permalink

Hi Keitaro,

Use the "cartoon_highlight_color" setting. For example:

set cartoon_highlight_color, red

Cheers,

-- Jason

On Sun, Mar 6, 2011 at 10:01 AM, Keitaro Yamashita

Post by Keitaro Yamashita
Dear all,
Can PyMOL set different colors on each side of cartoon strand?
I tried cartoon_discrete_colors but it was not for this purpose.
(I mean the sides from which sidechains are protruded.)
Thanks in advance,
Keitaro
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Keitaro Yamashita

2011-03-07 00:32:14 UTC

Permalink

Dear all,

Sorry for my unclear explanation.

I made a picture explaining what I'd like to do.
I want to color the front and back of sheets separately.

Jason said it should be possible, could anyone tell me how to do it?

Cheers,

Keitaro

Post by Jason Vertrees
Hi Keitaro,
set cartoon_highlight_color, red
Cheers,
-- Jason
On Sun, Mar 6, 2011 at 10:01 AM, Keitaro Yamashita

--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(o) +1 (603) 374-7120

Schubert, Carsten [PRDUS]

2011-03-07 15:12:06 UTC

Permalink

Not sure if this is possible but it would be a nice feature to have. Since it mimics the way helices are drawn, when cartoon_highlight_color is set.

Cheers,

Carsten

-----Original Message-----
Sent: Sunday, March 06, 2011 7:32 PM
Subject: Re: [PyMOL] Different color on each side of strand
Dear all,
Sorry for my unclear explanation.
I made a picture explaining what I'd like to do.
I want to color the front and back of sheets separately.
Jason said it should be possible, could anyone tell me how to do it?
Cheers,
Keitaro

Post by Jason Vertrees
Hi Keitaro,
set cartoon_highlight_color, red
Cheers,
-- Jason
On Sun, Mar 6, 2011 at 10:01 AM, Keitaro Yamashita

Post by Jason Vertrees

Post by Keitaro Yamashita
--------- What You Don't Know About Data Connectivity CAN Hurt You
This paper provides an overview of data connectivity, details its
effect on application quality, and explores various alternative
solutions. http://p.sf.net/sfu/progress-d2d
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users

--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(o) +1 (603) 374-7120

Hongbo Zhu

2011-03-07 15:48:14 UTC

Permalink

how do you define "front" and "back" sides of sheets in general?

Post by Keitaro Yamashita
Dear all,
Sorry for my unclear explanation.
I made a picture explaining what I'd like to do.
I want to color the front and back of sheets separately.
Jason said it should be possible, could anyone tell me how to do it?
Cheers,
Keitaro

Post by Jason Vertrees
Hi Keitaro,
set cartoon_highlight_color, red
Cheers,
-- Jason
On Sun, Mar 6, 2011 at 10:01 AM, Keitaro Yamashita

--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
What You Don't Know About Data Connectivity CAN Hurt You
This paper provides an overview of data connectivity, details
its effect on application quality, and explores various alternative
solutions. http://p.sf.net/sfu/progress-d2d
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users

Keitaro Yamashita

2011-03-08 02:11:30 UTC

Permalink

Dear Hongbo,

For example, user can put something like light source and "front" is
defined as the side light hits.
(though it would be undefined If sheet plane is placed parallel to the ray..)

But I think any definition is ok if front and back could be alternated
easily by user operation.

Cheers,

Keitaro

Post by Hongbo Zhu
how do you define "front" and "back" sides of sheets in general?

Hongbo Zhu

2011-03-08 07:52:31 UTC

Permalink

Hi, Keitaro,

Post by Keitaro Yamashita
Dear Hongbo,
For example, user can put something like light source and "front" is
defined as the side light hits.
(though it would be undefined If sheet plane is placed parallel to the ray..)

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Keitaro Yamashita
But I think any definition is ok if front and back could be alternated
easily by user operation.

sounds like an interesting operation, though.

Post by Keitaro Yamashita
Cheers,
Keitaro

Post by Hongbo Zhu
how do you define "front" and "back" sides of sheets in general?

------------------------------------------------------------------------------
What You Don't Know About Data Connectivity CAN Hurt You
This paper provides an overview of data connectivity, details
its effect on application quality, and explores various alternative
solutions. http://p.sf.net/sfu/progress-d2d
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users

Keitaro Yamashita

2011-03-08 09:16:10 UTC

Permalink

Dear Hongbo,

Post by Hongbo Zhu

Post by Keitaro Yamashita
For example, user can put something like light source and "front" is
defined as the side light hits.
(though it would be undefined If sheet plane is placed parallel to the ray..)

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

I think this definition is useful when color e.g. beta-barrel, but
definitely includes ambiguity.
Then, how about defining front side as the C-beta direction of
starting residue of sheet?

Cheers,

Keitaro

Post by Hongbo Zhu
Hi, Keitaro,

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Keitaro Yamashita
But I think any definition is ok if front and back could be alternated
easily by user operation.

sounds like an interesting operation, though.

Post by Keitaro Yamashita
Cheers,
Keitaro

Post by Hongbo Zhu
how do you define "front" and "back" sides of sheets in general?

--
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail: hongbo.zhu at biotec
Webpage: www.biotec.tu-dresden.de
------------------------------------------------------------------------------
What You Don't Know About Data Connectivity CAN Hurt You
This paper provides an overview of data connectivity, details
its effect on application quality, and explores various alternative
solutions. http://p.sf.net/sfu/progress-d2d
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users

Hongbo Zhu

2011-03-08 10:12:32 UTC

Permalink

I like the idea about coloring tim-barrels.

At the moment the secondary structures can be selected in PyMOL using
selector "ss". I wonder whether it makes sense to label each strand with
an index so we can select each strand individually, e.g.

select ss s5 # select the 5th strand from the N-term

and then one can flip the colors of the two "sides" of the strand in
case it is not colored properly according to the user.

hongbo

Post by Keitaro Yamashita
Dear Hongbo,

Post by Hongbo Zhu

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Hongbo Zhu
Hi, Keitaro,

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Keitaro Yamashita
But I think any definition is ok if front and back could be alternated
easily by user operation.

sounds like an interesting operation, though.

Post by Keitaro Yamashita
Cheers,
Keitaro

Post by Hongbo Zhu
how do you define "front" and "back" sides of sheets in general?

gilleain torrance

2011-03-08 10:50:57 UTC

Permalink

Hi,

Although most of the time the strands in a sheet have clear 'sides',
this won't always be true. Keitaro already mentioned the possibility
of twisted strands, but you can also get two sheets that share the
'same' long strand - well, depending on the SSE assignment algorithm,
I suppose.

Jellyrolls (http://www.cathdb.info/cathnode/2.60.120) are an example
of this, I seem to remember, as they have long strands that cross from
one sheet to another. As the sheets are in a sandwich, the strand will
change side halfway through.

This coloring scheme still sounds like it would be useful, but there
might be some odd visual effects, or an algorithm to take care of
corner cases.

gilleain

On Tue, Mar 8, 2011 at 10:12 AM, Hongbo Zhu

Post by Hongbo Zhu
I like the idea about coloring tim-barrels.
At the moment the secondary structures can be selected in PyMOL using
selector "ss". I wonder whether it makes sense to label each strand with
an index so we can select each strand individually, e.g.
select ss s5 # select the 5th strand from the N-term
and then one can flip the colors of the two "sides" of the strand in
case it is not colored properly according to the user.
hongbo

Post by Keitaro Yamashita
Dear Hongbo,

Post by Hongbo Zhu

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Hongbo Zhu
Hi, Keitaro,

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Keitaro Yamashita
But I think any definition is ok if front and back could be alternated
easily by user operation.

sounds like an interesting operation, though.

Post by Keitaro Yamashita
Cheers,
Keitaro

Post by Hongbo Zhu
how do you define "front" and "back" sides of sheets in general?

Keitaro Yamashita

2011-03-09 14:22:33 UTC

Permalink

Hi,

Yes, there're definitely a few (?) exceptional cases.
But maybe people don't use this feature in such case.

Anyway, this feature is not included in current PyMOL, right?
Then, is it hard to implement this feature (many changes in code required)?

Keitaro

Post by gilleain torrance
Hi,
Although most of the time the strands in a sheet have clear 'sides',
this won't always be true. Keitaro already mentioned the possibility
of twisted strands, but you can also get two sheets that share the
'same' long strand - well, depending on the SSE assignment algorithm,
I suppose.
Jellyrolls (http://www.cathdb.info/cathnode/2.60.120) are an example
of this, I seem to remember, as they have long strands that cross from
one sheet to another. As the sheets are in a sandwich, the strand will
change side halfway through.
This coloring scheme still sounds like it would be useful, but there
might be some odd visual effects, or an algorithm to take care of
corner cases.
gilleain
On Tue, Mar 8, 2011 at 10:12 AM, Hongbo Zhu

Post by Keitaro Yamashita
Dear Hongbo,

Post by Hongbo Zhu

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Hongbo Zhu
Hi, Keitaro,

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Keitaro Yamashita
But I think any definition is ok if front and back could be alternated
easily by user operation.

sounds like an interesting operation, though.

Post by Keitaro Yamashita
Cheers,
Keitaro

Post by Hongbo Zhu
how do you define "front" and "back" sides of sheets in general?

Tsjerk Wassenaar

2011-03-09 15:03:37 UTC

Permalink

Hi Keitaro,

You can try to create a copy from the piece containing the sheet,
colour it differently, and change the coordinates slightly. It's a bit
tricky maybe, especially if you've got quite a bit of curvature.

Hope it helps,

Tsjerk

On Wed, Mar 9, 211 at 3:22 PM, Keitaro Yamashita

Post by Keitaro Yamashita
Hi,
Yes, there're definitely a few (?) exceptional cases.
But maybe people don't use this feature in such case.
Anyway, this feature is not included in current PyMOL, right?
Then, is it hard to implement this feature (many changes in code required)?
Keitaro

Post by Keitaro Yamashita
Dear Hongbo,

Post by Hongbo Zhu

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Hongbo Zhu
Hi, Keitaro,

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Keitaro Yamashita
But I think any definition is ok if front and back could be alternated
easily by user operation.

sounds like an interesting operation, though.

Post by Keitaro Yamashita
Cheers,
Keitaro

Post by Hongbo Zhu
how do you define "front" and "back" sides of sheets in general?

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

Hongbo Zhu

2011-03-09 15:52:27 UTC

Permalink

I was also thinking along that line :) But that is pretty trick for a
structure like beta-barrel, since you have to actually shrink the barrel
toward the center.

here is another hack that might work:

1. render only the black outline of the cartoon representation of your
protein:
set ray_trace_mode,2 # see http://www.pymolwiki.org/index.php/Ray

2. fill the cartoon, especially the beta strands using different colors
using some image manipulation program (a great example is GIMP). This is
fairly easy as most of such programs provide a "Fill Tool" (in GIMP it
is the bucket button). Using such a tool you have the picture in a few
clicks. I have actually made an example of a beta barrel (1opfA):

http://www.biotec.tu-dresden.de/~hongboz/pymol_example/1opfA.html

(In this quick example, I have oriented the protein such that both sides
of some strands can be seen.)

hongbo

Post by Jason Vertrees
Hi Keitaro,
You can try to create a copy from the piece containing the sheet,
colour it differently, and change the coordinates slightly. It's a bit
tricky maybe, especially if you've got quite a bit of curvature.
Hope it helps,
Tsjerk
On Wed, Mar 9, 211 at 3:22 PM, Keitaro Yamashita

Post by Keitaro Yamashita
Dear Hongbo,

Post by Hongbo Zhu

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Hongbo Zhu
Hi, Keitaro,

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Keitaro Yamashita
But I think any definition is ok if front and back could be alternated
easily by user operation.

sounds like an interesting operation, though.

Post by Keitaro Yamashita
Cheers,
Keitaro

Post by Hongbo Zhu
how do you define "front" and "back" sides of sheets in general?

Keitaro Yamashita

2011-03-11 12:48:00 UTC

Permalink

Dear Tsjerk and Hongbo,

Thank you very much for giving me ideas.

As mentioned by Honbo, I think shifting strand can work in only case
of very planar strand.

I'll try painting strands with GIMP -- thank you for your kindness!

Keitaro

Post by Hongbo Zhu
I was also thinking along that line :) But that is pretty trick for a
structure like beta-barrel, since you have to actually shrink the barrel
toward the center.
1. render only the black outline of the cartoon representation of your
set ray_trace_mode,2 # see http://www.pymolwiki.org/index.php/Ray
2. fill the cartoon, especially the beta strands using different colors
using some image manipulation program (a great example is GIMP). This is
fairly easy as most of such programs provide a "Fill Tool" (in GIMP it
is the bucket button). Using such a tool you have the picture in a few
http://www.biotec.tu-dresden.de/~hongboz/pymol_example/1opfA.html
(In this quick example, I have oriented the protein such that both sides
of some strands can be seen.)
hongbo

Post by Keitaro Yamashita
Dear Hongbo,

Post by Hongbo Zhu

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Hongbo Zhu
Hi, Keitaro,

and even the same strand can have half of it facing the light source and
the other half turned opposite to the source.

Post by Keitaro Yamashita
But I think any definition is ok if front and back could be alternated
easily by user operation.

sounds like an interesting operation, though.

Post by Keitaro Yamashita
Cheers,
Keitaro

Post by Hongbo Zhu
how do you define "front" and "back" sides of sheets in general?

--
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail: hongbo.zhu at biotec
Webpage: www.biotec.tu-dresden.de
------------------------------------------------------------------------------
Colocation vs. Managed Hosting
A question and answer guide to determining the best fit
for your organization - today and in the future.
http://p.sf.net/sfu/internap-sfd2d
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users

Maia Cherney

2011-03-13 06:06:41 UTC

Permalink

Hello,

I have an old saved session as a pse file. How can I save a script that
produced that pse file. It may be easier just to get information about
each object in that pse file.

Maia

Schubert, Carsten [PRDUS]

2011-03-13 10:01:45 UTC

Permalink

Maia,

as far as I know a .pse is just a dump of the internal data structure of
Pymol. You can save the molecules contained in the session, but the
graphical representation and any modifications would need to be
recreated.
Hopefully Jason proves me wrong ...

Cheers,

Carsten

-----Original Message-----
Sent: Sunday, March 13, 2011 7:07 AM
To: Jason Vertrees
Subject: Re: [PyMOL] write a script from pse file
Hello,
I have an old saved session as a pse file. How can I save a script that
produced that pse file. It may be easier just to get information about
each object in that pse file.
Maia

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http://www.mail-archive.com/pymol-***@lists.sourceforge.net

Tsjerk Wassenaar

2011-03-13 10:36:12 UTC

Permalink

Hi,

Well, a .pse file indeed is a kind of dump. But it does contain the
information, of which most can be extracted. To begin with, it is quite
trivial to get a listing of the settings (get) and of the view (get_view).
It is also possible to obtain the color per atom, for which code is
somewhere in the archives and maybe on the wiki. The real problem is the
representation. All in all, it is a bit cumbersome. So before attempting to
script something... how necessary is it? What's the underlying problem to be
solved?

Cheers,

Tsjerk

On Mar 13, 2011 11:04 AM, "Schubert, Carsten [PRDUS]" <***@its.jnj.com>
wrote:

Maia,

as far as I know a .pse is just a dump of the internal data structure of
Pymol. You can save the molecules contained in the session, but the
graphical representation and any modifications would need to be
recreated.
Hopefully Jason proves me wrong ...

Cheers,

Carsten

Sent: Sunday, March ...

Maia Cherney

2011-03-13 16:34:57 UTC

Permalink

Hi,
My major problem is hydrogen bonds (hb). Under each hb1, or hb2, .. hb10
there are many hbs, (not just one individual hb). I want a list of them
for each hb. Now how can I use "get " to see all hbs in hb1, etc? I need
to make a table of all hydrogen bonds for this pse.

Maia

Post by Tsjerk Wassenaar
Hi,
Well, a .pse file indeed is a kind of dump. But it does contain the
information, of which most can be extracted. To begin with, it is
quite trivial to get a listing of the settings (get) and of the view
(get_view). It is also possible to obtain the color per atom, for
which code is somewhere in the archives and maybe on the wiki. The
real problem is the representation. All in all, it is a bit
cumbersome. So before attempting to script something... how necessary
is it? What's the underlying problem to be solved?
Cheers,
Tsjerk

Post by Tsjerk Wassenaar
On Mar 13, 2011 11:04 AM, "Schubert, Carsten [PRDUS]"
Maia,
as far as I know a .pse is just a dump of the internal data structure of
Pymol. You can save the molecules contained in the session, but the
graphical representation and any modifications would need to be
recreated.
Hopefully Jason proves me wrong ...
Cheers,
Carsten

-----Original Message----- > From: Maia Cherney

March ...