[Chimera-users] No mmcif module in ChimeraX 1.0?

Eric Pettersen pett at cgl.ucsf.edu
Tue Feb 23 13:59:05 PST 2021

Hi Yangqi,

> On Feb 23, 2021, at 8:34 AM, Yangqi Gu <yangqi.gu at yale.edu> wrote:
> Dear Chimera Developer,
> I am trying to use an external python script to run some calculations. I am using ChimeraX 1.0 and the script requires the import of mmcif module but apparently it is not installed in ChimeraX 1.0? How should I install this module?

The mmcif module is chimerax.mmcif in all versions of ChimeraX.  The more pertinent question is why would you need this module explicitly?  Wouldn't you just run the "open" command, e.g.:

	from chimerax.core.commands import run
	models = run(session, "open /path/to/file.cif")

> I also downloaded a newer version 1.1, but it is a precompiled version.

1.1 is no more "precompiled" than 1.0 was.

> Do I need to remove ChimeraX 1.0? Because the older version was installed in /usr/bin with an executable file, but for the newer version, I assume I need to add the path for the executables?

Just nuke 1.0.  There is no reason to keep it around.

> I also need to run some ISODLE refinement with my gpu, will ChimeraX configure gpu automatically?

AFAIK, ISOLDE will automatically use the GPU for the most part.


	Eric Pettersen
	UCSF Computer Graphics Lab

> Best,
> Yangqi
> -- 
> Yangqi Gu
> Graduate Student
> Malvankar Lab
> Yale University, West Campus
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