Hi ABhik -
You'll want to have a look at the `split_states` command. Something like the
following should get you going. Note the embedded multiline `python` block.
# Using 1nmr as a sample structure
fetch 1nmr, async=0
split_states 1nmr, prefix=model
python
# starting at state 2, align each model to state 1
for i in range(2, cmd.count_states('1nmr') + 1):
this_model = 'model{:04d}'.format(i)
cmd.super(this_model, 'model0001')
cmd.save('{}.pdb'.format(this_model), this_model)
python end
For your 100000 structures you'll also need more zero-padding (e.g. '{:07d}').
You can save this as super_states.pml and run from PyMOL with the command:
@super_states.pml
Hope that helps.
Cheers,
Jared
On July 30, 2018 at 2:16:54 AM, abhik.gh...@bose.res.in
(abhik.gh...@bose.res.in) wrote:
Hello All
I have a pdb file containing 100000 frames . Now I want to align all frame
one by one in pymol and then want to save the final coordinate. How it can
be done?
All suggestions are welcome
Thanking you.
ABhik
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