HI Abdul,
Not sure if this is the solution you would like to, but there are several tools
which are tailored specifically for this purpose (i.e. superimposition of small
molecules). One of them is SiteBinder
(http://webchem.ncbr.muni.cz/Platform/App/SiteBinder), it allows you to do
variety of superimpositions and the results can be loaded back to PyMOl. If you
need further assistance with SiteBInder, just let me know.
Cheers
Lukas
From: Abdul Ajees [mailto:a_abdul_aj...@yahoo.com]
Sent: Saturday, February 7, 2015 7:46 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] ligand superimpose (multiple structures) and RMSD value
Dear Pymol users and developers,
I need to superimpose more than 200 ligands (same ligand with different
conformations) to one target ligand and obtain the RMSD value.
for example
align 1RGS.pdb 1KMS.pdb
align 1VKS.pdb 1KMS.pdb
align 1CHC.pdb 1KMS.pdb
.......
......
I can manually do this action but it take long time. Is there a way to do this
action quick and automatic using pymol ? For your kind information, I have
pymol windows and linux version.
My idea is to group the 200 ligands into various groups based on their
conformation. I found some scripts at
"http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/";. But it is not working
for me.
It will be highly beneficial to me, if you could kindly suggest any idea.
Thank you,
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