[PyMOL] Changing ligand conformation

[Mark Bostock]

I have a pdb file of a protein which contains a lysine residue bound to
a ligand. The ligand has two conformations due to a cis/trans
isomerisation. I have created a pdb file (also .mol and .mol2) of lysine
attached to the cis form and would like to replace the
lysine-ligand(trans) form which is currently in the protein structure
with the lysine-ligand(cis) form. Does anyone know how to do this;
mutagenesis only gives me the option of standard amino acids and also
does not remove the existing ligand.

Many thanks,

Mark.

[Jason Vertrees]

Hi Mark,

It sounds like you have a couple options. First, you could use PyMOL's
builder (http://www.pymolwiki.org/index.php/Builder; the page needs
updating) to do the trans->cis conversion yourself, by hand. Second,
if you already have the cis structure coordinates, you could issue the
"update" command with the cis coordinates on the trans conformer. Type
"help update" to get help on the update command. The PyMOLWiki has
some more information here: http://www.pymolwiki.org/index.php/Update.

Cheers,

-- Jason

Post by Mark Bostock
I have a pdb file of a protein which contains a lysine residue bound to
a ligand. The ligand has two conformations due to a cis/trans
isomerisation. I have created a pdb file (also .mol and .mol2) of lysine
attached to the cis form and would like to replace the
lysine-ligand(trans) form which is currently in the protein structure
with the lysine-ligand(cis) form. Does anyone know how to do this;
mutagenesis only gives me the option of standard amino acids and also
does not remove the existing ligand.
Many thanks,
Mark.
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[Mark Bostock]

I have pymol 1.5 installed on windows 7 (32 bit). The install works fine
with .pdb files, however if I try to open a session file (.pse) created
on another machine (windows xp, also running pymol 1.5) the software
crashes; there are no error messages in the pymol command line. The
programme just freezes (after attempting to resize the display) and then
windows tries to 'fix' the problem before the software crashes. Does
anyone have any experience of this issue. I've tried a complete
uninstall and reinstall but to no success.

Many thanks,

Mark

[Jason Vertrees]

Hi Mark,

PyMOL Session files store their settings. So, if you're running PyMOL
on a powerful desktop machine that has OpenGL shader-based technology
and then save that file, the high-performance graphics settings will
be saved. If you then try to open that session file on a low-end
laptop, say, when PyMOL tries to restore those high-end settings it
might crash because the computer isn't capable of handling those
settings.

We are working on making it such that PyMOL will override those stored
settings if your machine cannot handle them.

Before saving the session file, please try setting:
set use_shaders, 0
set sphere_mode, 0

That session file should be able to load anywhere.

Cheers,

-- Jason

Post by Mark Bostock
I have pymol 1.5 installed on windows 7 (32 bit). The install works fine
with .pdb files, however if I try to open a session file (.pse) created
on another machine (windows xp, also running pymol 1.5) the software
crashes; there are no error messages in the pymol command line. The
programme just freezes (after attempting to resize the display) and then
windows tries to 'fix' the problem before the software crashes. Does
anyone have any experience of this issue. I've tried a complete
uninstall and reinstall but to no success.
Many thanks,
Mark
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[Joel Tyndall]

Mark,

You could always simply edit the pdb file (remove the trans option). Simply open up the pdb file in a text editor (gedit/notetab/wordpad) and delete the lines corresponding to the trans form. The pdb file (compare with the mol or mol2 files) is simple to edit manually. The others require connectivity etc to be edited.

The last pdb file I saw with an alt conf looked like this:

ATOM 53 CG2AVAL A 6 -5.306 -11.323 22.865 0.50 11.50 A C
ATOM 54 CG2BVAL A 6 -7.334 -10.108 21.413 0.50 12.94 A C
ATOM 55 C VAL A 6 -8.805 -10.428 23.682 1.00 11.53 A C
ATOM 56 O VAL A 6 -9.347 -11.540 23.573 1.00 12.73 A O

Where the AVAL and BVal correspond to different orientations.

Hope this helps
_________________________________
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand  
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea               [phone]
Fax / Waeawhakaahua     [phone]


-----Original Message-----
From: Mark Bostock [mailto:***@cam.ac.uk]
Sent: Saturday, 10 December 2011 10:26 a.m.
To: pymol-***@lists.sourceforge.net
Subject: [PyMOL] Changing ligand conformation

I have a pdb file of a protein which contains a lysine residue bound to a ligand. The ligand has two conformations due to a cis/trans isomerisation. I have created a pdb file (also .mol and .mol2) of lysine attached to the cis form and would like to replace the
lysine-ligand(trans) form which is currently in the protein structure with the lysine-ligand(cis) form. Does anyone know how to do this; mutagenesis only gives me the option of standard amino acids and also does not remove the existing ligand.

Many thanks,

Mark.

[Troels Emtekær Linnet]

Or just use this script
http://www.pymolwiki.org/index.php/RemoveAlt

Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: [phone]

Post by Joel Tyndall
Mark,
You could always simply edit the pdb file (remove the trans option).
Simply open up the pdb file in a text editor (gedit/notetab/wordpad) and
delete the lines corresponding to the trans form. The pdb file (compare
with the mol or mol2 files) is simple to edit manually. The others require
connectivity etc to be edited.
ATOM 53 CG2AVAL A 6 -5.306 -11.323 22.865 0.50 11.50 A
C
ATOM 54 CG2BVAL A 6 -7.334 -10.108 21.413 0.50 12.94 A
C
ATOM 55 C VAL A 6 -8.805 -10.428 23.682 1.00 11.53
A C
ATOM 56 O VAL A 6 -9.347 -11.540 23.573 1.00 12.73
A O
Where the AVAL and BVal correspond to different orientations.
Hope this helps
_________________________________
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa
Ph / Waea [phone]
Fax / Waeawhakaahua [phone]
-----Original Message-----
Sent: Saturday, 10 December 2011 10:26 a.m.
Subject: [PyMOL] Changing ligand conformation
I have a pdb file of a protein which contains a lysine residue bound to a
ligand. The ligand has two conformations due to a cis/trans isomerisation.
I have created a pdb file (also .mol and .mol2) of lysine attached to the
cis form and would like to replace the
lysine-ligand(trans) form which is currently in the protein structure with
the lysine-ligand(cis) form. Does anyone know how to do this; mutagenesis
only gives me the option of standard amino acids and also does not remove
the existing ligand.
Many thanks,
Mark.
------------------------------------------------------------------------------
Cloud Services Checklist: Pricing and Packaging Optimization This white
paper is intended to serve as a reference, checklist and point of
discussion for anyone considering optimizing the pricing and packaging
model of a cloud services business. Read Now!
http://www.accelacomm.com/jaw/sfnl/114/51491232/
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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