Hi Pedro It does not work, the pymol crashes if I use this selection
Stéphane ---------------------------------------------------------- Stéphane Abel, Ph.D. CEA Centre de Saclay DRF/JOLIOT/I2BC-S/SB2SM/LBMS Bat 528, Office 138C Gif-sur-Yvette, F-91191 FRANCE Phone (portable) : +33 6 49 37 70 60 ________________________________________ De : Pedro Lacerda [pslace...@gmail.com] Envoyé : lundi 22 juin 2020 16:26 À : ABEL Stephane Cc : pymol-users Objet : Re: [PyMOL] Python script with iterate_state and selection command Hi, Not sure if I understood your code but maybe you want change Myselection to: Myselection="resname SOL within 3.5 of resname CHO" -- Pedro Lacerda Em seg, 22 de jun de 2020 10:44, ABEL Stephane <stephane.a...@cea.fr<mailto:stephane.a...@cea.fr>> escreveu: Hello all, I would like to write a basic python script to select residues for each state using the iterate_state and output the results first in pymol console window with the following format frame 1 : resid ... frame 2 : resid ... ... ### my script ## from pymol import cmd, stored mytraj="" mytraj2="" ## Load PDB cmd.load("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0ns.pdb"), mytraj ## Load XTC cmd.load_traj("1JNO_GrA_DMPC_NACL_Membrane_TIP3P_SemiIso_rep3_Water_InChannel_0_50ns_Every_0.5ns_TRANSLATED.xtc"), mytraj2 stored.resid = [] Myselection="select water_channel, resname SOL within 3.5 of resname CHO" nb_states=cmd.count_states(mytraj2) ---> Contains 102 states print(mytraj2, nb_states) state=1 for i in range (nb_states) : print(i) cmd.iterate_state (i, (Myselection), 'resid.append(resv)') ----> Should to ireate for all the states print("frame " + str(i) + ":" + str(stored.residues)) ---> Print the results of the Myselection command in the console ### But the first problem I have is the syntax of the iterate_state. I obtain the following error "Selector-Error: Invalid selection name "select". ( select water_channel, resname SOL within 3.5 of resname CHO )<--" When I put this selection command directly in Pymol, it works and i can obtain the desired waters that was near 3.5 A of the CHO over all the states . So What is the correct syntax for the selection with "iterate_state" ? And how to output the results again for each state in the screen . Thanks in advance for your help Stéphane _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
