pymol-users

[PyMOL] Changing ligand conformation

[Mark B. <mj...@ca...>]

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.

Re: [PyMOL] Changing ligand conformation

[Jason V. <jas...@sc...>]

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

On Fri, Dec 9, 2011 at 4:26 PM, Mark Bostock <mj...@ca...> wrote:
> 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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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Re: [PyMOL] Changing ligand conformation

[Joel T. <joe...@ot...>]

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

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Fax / Waeawhakaahua     +64 3 4797034


-----Original Message-----
From: Mark Bostock [mailto:mj...@ca...] 
Sent: Saturday, 10 December 2011 10:26 a.m.
To: pym...@li...
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.



------------------------------------------------------------------------------
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http://www.accelacomm.com/jaw/sfnl/114/51491232/
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Re: [PyMOL] Changing ligand conformation

[Troels E. L. <tl...@gm...>]

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

Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234



2011/12/13 Joel Tyndall <joe...@ot...>

> 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               +64 3 4797293
> Fax / Waeawhakaahua     +64 3 4797034
>
>
> -----Original Message-----
> From: Mark Bostock [mailto:mj...@ca...]
> Sent: Saturday, 10 December 2011 10:26 a.m.
> To: pym...@li...
> 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/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
> ------------------------------------------------------------------------------
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> Improve efficiency and utilization of IT resources. Drive out cost and
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>

[PyMOL] Software crashing when opening .pse files

[Mark B. <mj...@ca...>]

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

Re: [PyMOL] Software crashing when opening .pse files

[Jason V. <jas...@sc...>]

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

On Fri, Nov 2, 2012 at 4:14 PM, Mark Bostock <mj...@ca...> wrote:
> 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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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120