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>
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
>
>
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