Hello,

As Elaine said, you cannot "convert" between the two formats because they represent different things (a volume, atomic coordinates).

But you can generate a volume from atomic coordinates with the molmap command (think of it as producing a synthetic density map of the molecule): https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html

The inverse task of building an atomic model from a volume and a sequence, in an automated way, is still an open problem. But research on this problem is making fast progress these days, see for instance https://github.com/3dem/model-angelo https://github.com/3dem/model-angelo

Cheers,

Guillaume

On 5 Oct 2022, at 17:37, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi Tianming, No -- they are different kinds of data. MRC is a density-map format, PDB is an atomic structure format. Best, Elaine

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Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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On Oct 5, 2022, at 6:54 AM, Tianming Qu via ChimeraX-users chimerax-users@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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ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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.p... 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/m... 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_...

Tom

On Oct 6, 2022, at 7:04 AM, Tianming Qu via ChimeraX-users chimerax-users@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@cgl.ucsf.edu 日期: 星期三, 2022年10月5日 上午11:37 收件人: Tianming Qu tqu@fsu.edu 抄送: Tianming Qu via ChimeraX-users chimerax-users@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

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Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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On Oct 5, 2022, at 6:54 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi, is there any way I can convert a .mrc file to .pdb file in chimera?

Best, Tianming

---

ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users