[chimerax-users] mrc to pdb

[Tom Goddard]

Hi Tianming,

  It is pretty simple to compute the enclosed volume of a closed triangulated surface.  But the ChimeraX code is a bit more complicated because it finds any holes in the surface and tries to cap them off.  Here is the Python code for the ChimeraX measure volume command on github

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

(it is also distributed with your ChimeraX distribution, e.g. on Mac in ChimeraX.app/Contents/lib/python3.9/site-packages/chimerax/surface/area.py).  The actual calculation is done in C++ for speed and called from Python and that C++ code is on github here

        https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/surface/_surface/measure.cpp <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/surface/_surface/measure.cpp>

The Chimera Programming Manual has a list of the commands and documentation for the corresponding Python functions.  But "measure volume" is not yet documented.

	https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/core/src/commands/user_commands.html

  Tom


> On Oct 6, 2022, at 7:04 AM, Tianming Qu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi, 
> Thanks for the response.
> 
> One more question, how does the chimeraX calculate out the volume of a density map? I mean, I know how to do this operation through the tools-volume-measure volume, but I am curious what is the source code chimeraX used to calculate this volume.
>  
> Best,
> Tianming
> 发件人: Elaine Meng <meng at cgl.ucsf.edu>
> 日期: 星期三, 2022年10月5日 上午11:37
> 收件人: Tianming Qu <tqu at fsu.edu>
> 抄送: Tianming Qu via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
> 主题: Re: [chimerax-users] mrc to pdb
> 
> Hi Tianming,
> No -- they are different kinds of data.  MRC is a density-map format, PDB is an atomic structure format.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Oct 5, 2022, at 6:54 AM, Tianming Qu via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > 
> > Hi, is there any way I can convert a .mrc file to .pdb file in chimera?
> > 
> > Best,
> > Tianming 
> 
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