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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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<mailto: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<https://aka.ms/LearnAboutSenderIdentification> 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 [cid:image001.png@01D97789.6093E3B0] On Apr 25, 2023, at 9:12 AM, Eric Pettersen via Chimera-users <chimera-users@cgl.ucsf.edu<mailto: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