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
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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
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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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