Hi Greg, I am using ChimeraX 1.6 and the commands you list do not work: open<help:user/commands/open.html> cir fromDatabase ccd Unknown CCD ligand name open<help:user/commands/open.html> 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<https://aka.ms/LearnAboutSenderIdentification> 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: [cid:image001.png@01DA00D1.71BF7AB0] From: "Jaremko, Matt Joseph" <matt.jaremko@merck.com><mailto:matt.jaremko@merck.com> Date: Monday, October 16, 2023 at 11:45 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><mailto: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: [cid:image002.png@01DA00D1.71BF7AB0] 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<mailto:matt.jaremko@merck.com> 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<https://www.msd.com/contact-us/>.) 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. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ 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<https://www.msd.com/contact-us/>.) 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.
