[chimerax-users] ChimeraX Python Scripting for EM Maps

[Tom Goddard]

Hi Steven,

Elaine pointed to the right place for the fitmap Python documentation.  I've also added it under the Python Modules page under Volume data to make it easier to find.  The open_pdb() and save_pdb() functions are here and have strangely not been documented.

	https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/pdb/src/pdb.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/pdb/src/pdb.py>

We will try to get those documented in the Programmer's manual.

ChimeraX fitting of atomic models in maps is intended for interactive fitting.  Keep that in mind if you are going to try to script it in Python.  It doesn't have good capabilities for doing global searches and is really intended to locally optimize a fit once you have atomic models close to their correct positions.

	Tom

> On Feb 19, 2021, at 10:29 AM, Elaine Meng <meng at cgl.ucsf.edu> wrotey:
> 
> Hi Steven,
> Maybe this page in the programmer documentation (and links therein) would help... it includes "fitmap," at least:
> 
> <https://www.cgl.ucsf.edu/chimerax/docs/devel/core/commands/user_commands.html>
> 
> I don't create the programmer documentation, but since the page says version 1.2 I'm hoping it's reasonably up-to-date.
> 
> The "save" link doesn't say much, however, so somebody else will have to give more information on writing files.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Feb 19, 2021, at 10:05 AM, Steven Truong <sdt45 at cam.ac.uk> wrote:
>> 
>> To whom it may concern,
>> Hello!  I was hoping to ask for some help in Python Scripting in ChimeraX.  Specifically, I am trying to fit structure files (.PDB) to electron density maps (.MAP).  Is there a way to do this in .PY scripts in ChimeraX?  I can’t seem to find such a command like “fitmap” in the documentation here (https://www.cgl.ucsf.edu/chimerax/docs/devel/modules.html).  Additionally, it seems like the “Read and Write PDB Files” page (https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/pdbio.html) of the documentation page hasn’t been updated.  Is there another place that outlines how to save structures?
> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210219/b0e1853a/attachment.html>