For the moment, you'd need to do this once for each file (changing the filename of course), but our next major release (2.11.3) has a much more powerful command line interface that supports batch processing of whole directories, globs and replacement. See Jalview develop's built in documentation after launching it to find out more (https://www.jalview.org/development/jalview_develop/).

From: Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: 28 June 2023 18:35
To: Eric Pettersen <pett@cgl.ucsf.edu>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] Re: Save only the sequence that is present in the model

Hi Matthias,

There is no command for just saving the modeled sequence of a structure, so you would have to use Python scripting. Below is the code to print the names of chains and the corresponding modeled sequences to the log. You should be able to easily adapt it to what you want, assuming you're familiar with Python...

from chimerax.atomic import all_atomic_structures

for s in all_atomic_structures(session):

for chain in s.chains:

print(chain.name, ''.join([c for c, r in zip(chain.characters, chain.residues) if r]))

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Jun 28, 2023, at 8:29 AM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Begin forwarded message:

From: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at>

Subject: Save only the sequence that is present in the model

Date: June 28, 2023 at 6:53:11 AM PDT

To: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu>

Dear ChimeraX team,

I would like to save only the sequence of a chain that is actually modelled. As I would like to do this for many files it would be great if this would work via scripting. Is this possible?

Many thanks,

Matthias

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