[chimerax-users] Re: Open small molecule cif

The commands work for me in 1.6.  So this now sounds like a network connectivity issue.  ChimeraX fetches the CCD files from https://files.wwpdb.org/.   I wouldn't be surprised if your company has a https proxy or firewall that needs to be configured to allow that.  Please consult with your local IT folks and let us know what you find out.     -- Greg On 10/17/2023 5:10 AM, Jaremko, Matt Joseph wrote:

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 *Date: *Tuesday, October 17, 2023 at 2:51 AM *To: *"Jaremko, Matt Joseph" , ChimeraX Users Help *Subject: *Re: [chimerax-users] Re: Open small molecule cif

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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:

*From: *"Jaremko, Matt Joseph" mailto:matt.jaremko@merck.com *Date: *Monday, October 16, 2023 at 11:45 AM *To: *ChimeraX Users Help 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:

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

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