From: ABEL S. <Ste...@ce...> - 2020-06-17 14:58:59
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Hello PyMOLers I have PDB file that contains different frames ( or state or models) extracted from a MD simulation and I would like to select the number the water near (say 3.5 Angstroms) a protein for each state and write the results in the file. For instance like this where resid is a list of the water that satisfy the cut off below Frame 0 : residX, residY, ...., Frame 1: residZ, residY, ...., In the pml script I have selected the water molecules near the protein within the pymol commands below ### select GrA_Channel, (id 1-267+277-542) and name CA+C+O+N select water_channel, resname SOL within 3.5 of GrA_Channel f=open("toto.txt","w") iterate_state 0, water_channel, state + ':' + water_channel ") ## How to use this command f.close() but I do not know to use the iterate_state for each frame with above selected command Can you help me ? Thank you in advance Stéphane |