Hi Matt, Both of those commands work for me in ChimeraX version 1.6.1 as well as a recent 1.7 daily build. However, I see that CCD fetch was added way back in version 1.0, so I doubt that version is an issue. Are you able to open anything from CCD? E.g. open ccd:tyr Does capitalizing the residue name help? open ccd:TYR ... actually, can you do any web fetch? E.g. PDB entries open 2d2n Although the error message does not suggest it, maybe there is some issue with web proxy settings, see the ChimeraX preferences, Web Access section: <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#webaccess> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 17, 2023, at 5:10 AM, Jaremko, Matt Joseph via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Greg, I am using ChimeraX 1.6 and the commands you list do not work:
open cir fromDatabase ccd Unknown CCD ligand name open ccd:cir Unknown CCD ligand name
How can I import these small molecule cifs from a file? This doesn’t seem to be working in 1.6.
Thank you, Matt
From: Greg Couch <gregc@cgl.ucsf.edu> Date: Tuesday, October 17, 2023 at 2:51 AM To: "Jaremko, Matt Joseph" <matt.jaremko@merck.com>, ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Re: Open small molecule cif
You don't often get email from gregc@cgl.ucsf.edu. Learn why this is important EXTERNAL EMAIL– Use caution with any links or file attachments. We added small molecule cif support in ChimeraX 1.6. So you need to update your version of ChimeraX. If a .cif file isn't a mmCIF, it will try to open it as a small molecule cif file. And, in your case, you can open the CIR ligand without downloading it first with:
open cir from ccd
or:
open ccd:cir
ccd stands for the PDB's Chemical Component Dictionary that has all of the PDB's residue information, including the ligands.
-- Greg
On 10/16/2023 8:47 AM, Jaremko, Matt Joseph via ChimeraX-users wrote: Sorry, this was the original error message: <image001.png>
From: "Jaremko, Matt Joseph" <matt.jaremko@merck.com> Date: Monday, October 16, 2023 at 11:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Open small molecule cif
Hello,
How do you open cifs for ligands? I’ve downloaded citrulline from the PDB database (attached), but I can’t open in ChimeraX: <image002.png>
Thank you, Matt
Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko@merck.com
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This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
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