Hi James -
For the first part, you should use split_states and super or cealign, as in my
response to one of your emails last month.
https://sourceforge.net/p/pymol/mailman/message/35156097/
Then, once you have aligned all the trajectory structures (let's say they're
called traj_01 through traj_10), you can create new objects from each of the
snapshots and the heme using the `or` operator in the selection passed to
`create`.
create heme_traj_01, traj_01 or resn HEM
create heme_traj_02, traj_02 or resn HEM
etc.
Hope that helps.
Cheers,
Jared
For 1, you need to get your MD simulatio
On Jul 12, 2016, at 3:05 AM, James Starlight
<jmsstarli...@gmail.com<mailto:jmsstarli...@gmail.com>> wrote:
Dear Pymol Users!
Here I desice to continue my topic regarding scripting in Pymol;
My current task:
I have 1 X-ray structure of cythochrome-C with HEME residue embedded
within the protein as a cofactor
I have 10 snapshots of cythochrome-C from MD trajectory where HEME was
not present explicitly
What I need from pymol to write some script, which will
1) align (superimpose) each MD snapshot againt reference
2) copy HEME residue from reference to each of the superimpsoed
snapshot within the same position.
Thanks so much for any suggestions regarding realization !
James
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