Hi Elaine,

That worked well. Thanks so much for your help!

Steve

~~~~~~~~~~~~~~~~~~~~~~~

Steven T. Frey

Associate Professor

Skidmore College

Department of Chemistry

815 North Broadway

Saratoga Springs, NY 12866

Phone: 518-580-5124

Email: sfrey@skidmore.edu

From: Elaine Meng <meng@cgl.ucsf.edu>
Date: Tuesday, April 25, 2023 at 12:43 PM
To: Steven Frey <sfrey@skidmore.edu>
Cc: chimera-users@cgl.ucsf.edu List <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] Can't open a cif file

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ChimeraX homepage and download page for your convenience

<https://www.rbvi.ucsf.edu/chimerax/index.html>
<https://www.rbvi.ucsf.edu/chimerax/download.html>

Elaine

> On Apr 25, 2023, at 9:39 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Hi Steve,
> ChimeraX does not have the thermal ellipsoids option currently.  However, in ChimeraX you can open your small-molecule CIF and then save it as PDB, e.g. ChimeraX commands:
>
> open 1853486.cif format corecif
> save 1853486.pdb
>
> (the filenames could be pathnames if not in the default location, e.g. ~/Desktop/ on Mac)
>
> The PDB file contains the ANISOU records needed for thermal ellipsoid display in Chimera.  You can open it in Chimera and use menu: Tools... Structure Analysis... Thermal Ellipsoids. In my tests of this process, I had to increase the scale factor (e.g. to 2.5) because with scale factor 1 they were too small to protrude from the sticks.  See attached image.
>
> I  hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> <ortep.png>
>
>
>> On Apr 25, 2023, at 9:12 AM, Eric Pettersen via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>>
>> Hi Steven,
>>      Chimera cannot handle small-molecule CIF files, only macromolecular CIF (mmCIF) files.  You could try our ChimeraX program (in particular the 1.6 release candidate) which can handle many small-molecule CIFs.  https://www.cgl.ucsf.edu/chimerax/
>>
>> --Eric
>>
>>      Eric Pettersen
>>      UCSF Computer Graphics Lab
>>
>>
>>> On Apr 25, 2023, at 6:25 AM, Steven Frey via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>>>
>>> Dear Chimera Team,
>>>
>>> I’m unable to open the CIF file for a structure that we had done in 2018 and am getting the error shown on the attached jpeg. I am also attaching the CIF file downloaded from CCSD which comes from our original paper:
>>>
>>> Steven T. Frey, Hillary A. Ramirez*, Manpreet Kauer, and Jerry P. Jasinski.  “Crystal structure of a seven-coordinate manganese(II) complex with tris(pyridin-2-ylmethyl)amine (TMPA),” Acta Crystallographica, 2018, E74, 1075-1078. https://doi.org/10.1107/S2056989018009611.
>>>
>>> I’d like to be able to open the file in Chimera so that I can produce an ORTEP drawing for another paper. Can you help me figure out what the problem is?
>>>
>>> Thanks, Steve Frey
>
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