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 ----- 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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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.p...> (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/m...> 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 ----- 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@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