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
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Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

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-----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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