Re: [PyMOL] allign multiple freme in pymol
Hi Abhik and Jared,
There is also "intra_fit" and "multifilesave":
https://pymolwiki.org/index.php/intra_fit
https://pymolwiki.org/index.php/multifilesave
Example:
intra_fit name CA
multifilesave model{state:06}.pdb, state=0
Cheers,
Thomas
> On Jul 30, 2018, at 9:46 PM, Jared Sampson wrote:
>
> 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 10 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 10 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
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] allign multiple freme in pymol
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 10 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 10 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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engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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[PyMOL] allign multiple freme in pymol
Hello All I have a pdb file containing 10 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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
