Re: [PyMOL] allign multiple freme in pymol

[Thomas H. <tho...@sc...>]

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 <jar...@co...> 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 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, abh...@bo... (abh...@bo...) 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 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.