Hello,
I am having trouble running scripts which vary selections on different
states of a PyMOL object. I've converted an MD trajectory into a pdb
with 500 models that PyMOL loads as 500 states of 1 object. For example,
I would then like to run the anglesbetweenhelices.py script (from PyMOL
wiki) on each state separately. A simple script example:
import anglebetweenhelices as abh
cmd.load('output.pdb', object="cdp")
for i in range(1,501):
cmd.set('state',i,'cdp')
cmd.select('hel1','/cdp///1-22')
cmd.select('hel2','/cdp///25-37')
x=abh.angle_between_helices('hel1','hel2', visualize=0, quiet=1)
print x
In theory the select command has a state option but this doesn't seem to
work (as is confirmed by
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg08224.html).
I then tried using the set state command, but this also does not seem to
affect the actual coordinates of the selection. The only thing that does
work is if in the GUI I go to the desired state by pressing the "<" and
">" animation buttons. But is there a way to select the state from
within a script?
Thanks!
Pawel
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