[Chimera-users] Save trajectory file to PDB

[Yan Yi Li]

Thanks Eric and Elaine, your comments are helpful.

From: Eric Pettersen <pett at cgl.ucsf.edu>
Date: Friday, June 24, 2022 at 11:48 AM
To: Chimera <chimera-users at cgl.ucsf.edu>
Cc: Yan Yi Li <yy33li at uwaterloo.ca>
Subject: Re: [Chimera-users] Save trajectory file to PDB
Also, most MD programs have utilities for generating PDB files directly from trajectory files.  Amber has cpptraj.  Gromac has "gmx trjconv".  You should investigate whether the MD package you are using has something similar.

--Eric

        Eric Pettersen
        UCSF Computer Graphics Lab


> On Jun 24, 2022, at 8:34 AM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hi Yan Li,
> You would have to open the trajectory in Chimera before you save a file, and to open the file, you would have to use MD Movie.
>
> However, you can do it all with Chimera commands if you put the input filename(s) in a MD Movie metafile and then open the metafile with the "open" command, then "coordset" to play through all the frames that you want to save in MD Movie to make sure that they have been read (or to go to a specific frame if you only want to save that one), and then use the "write" command to save the PDB.  See links below for details of each.
>
> (I do not know how to do it in python, somebody else would have to advise on that.)
>
> Explanation of MD Movie metafile
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html>
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#metafile>
>
> coordset command
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
>
> write command
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>> On Jun 24, 2022, at 6:28 AM, Yan Yi Li via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>
>> Hello,
>> I have a question about saving specific frame from trajectory file to PDB. Instead of using MD movie, is there any module/command available so that I can convert the file format directly with python script?
>> Regards
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