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
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