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)?




Thomas Evangelidis

PhD student

University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens