Dear PyMOL users,
I would like to write into a single file the top scored ligand poses
obtained from flexible receptor sidechain docking with Vina. Then I would
like to open this file in PyMOL and visulaize these poses one-by-one. One
solution would be to write every receptor conformation and the respective
ligand pose as a MODEL unit in a multi-model .pdb file. However, that
solution is not effective in terms of memory and disk space. Therefore I
would like somehow to avoid writing the coordinates of the rigid part of
the receptor in each MODEL unit of the .pdb file. If I load two .pdb files,
one containing the rigid part of the receptor and the other all the
sidechain conformations and the respective ligand poses, then the flexible
amino acids will not be connected to the rigid protein. Does anyone have
any idea how to circumvent that problem (no necessarily by using the .pdb
format)?
thanks,
~Thomas
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======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tev...@pharm.uoa.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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