Hi Elaine,

Thanks so much for your quick reply (and the quick reply of others too)! I will give this a try.

All the best, 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 12:39 PM
To: Steven Frey <sfrey@skidmore.edu>
Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] Can't open a cif file

You don't often get email from meng@cgl.ucsf.edu. Learn why this is important

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

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