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
~~~~~~~~~~~~~~~~~~~~~~~ Steven T. Frey Associate Professor
Skidmore College Department of Chemistry 815 North Broadway Saratoga Springs, NY 12866 Phone: 518-580-5124 Email: sfrey@skidmore.edumailto:sfrey@skidmore.edu
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 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
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> <1853486.cif><IMG_4212.jpeg>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>
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
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
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
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.edumailto: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 [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
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
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
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.edumailto: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 importanthttps://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.edumailto: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
participants (3)
-
Elaine Meng
-
Eric Pettersen
-
Steven Frey