Fw: Problem opening local small-molecule CIF file

[Ute.Roehrig@…]

Hi all,

I guess this is a bug?

Best regards,
Ute

________________________________
From: Ute Roehrig <Ute.Roehrig@sib.swiss>
Sent: Monday, November 24, 2025 10:49
To: Mailing List <chimerax-users@cgl.ucsf.edu>
Subject: Problem opening local small-molecule CIF file

Hello,

I'm having problems opening a locally stored small-molecule cif file.

For example, the following runs without problems:
open ccd:pim

But if I download the file (PIM.cif) and try to open it with ChimeraX, I get an error:
open PIM.cif -> No mmCIF models found.
open PIM.cif format corecif -> No small molecule CIF models found. Perhaps this is a mmCIF file?
open PIM.cif format smallcif -> No small molecule CIF models found. Perhaps this is a mmCIF file?

Thank you in advance for your help,
Ute

[Elaine Meng]

I can confirm that it doesn't work when I go to RCSB page for pim,
​https://www.rcsb.org/ligand/PIM
...download PIM.cif (attached), and try to open it in ChimeraX.

[Greg Couch]

Let's be clear, this isn't a problem with a small molecule CIF file. It is a problem with mmCIF file that has no atoms and is just a chemical component template. The workaround is to use "open ccd:PIM" which fetches the template (may already be cached on the local disk). That converts the CCD template into a residue. For now, if you really want to download the file, instead of having ChimeraX download it for you, you could put the downloaded file in the $HOME/Downloads/ChimeraX/CCD/ directory. Then use "open ccd:PIM". "open PIM from ccd" also works.

When this bug is fixed, "open PIM.cif format ccd" will also work.

[Ute.Roehrig@…]

Hi Greg,

Thank you for your clarification.

To give you some context: we need CHARMM topologies and parameters for most ligands from the PDB/CCD. The only way to get their 3D coordinates, chemical structure (bond orders) and atom names is through their CIF files, because the SDF files do not contain the atom names. I wrote a script converting CIF into mol2 format, but it would be very useful to be able to directly open these CIF files or my own in ChimeraX and/or to convert them to mol2 with ChimeraX, keeping the bond order information. I understand these CIF files contain chemical compound templates instead of atoms, but they contain a lot of information including a 3D structure, and it would be great to be able to use this information.

Thank you in advance for your help,
Ute


________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, December 3, 2025 0:26
To: gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; Ute Roehrig <Ute.Roehrig@sib.swiss>
Subject: Re: [ChimeraX] #19464: Fw: Problem opening local small-molecule CIF file

#19464: Fw: Problem opening local small-molecule CIF file
------------------------------------+------------------------
          Reporter:  Ute.Roehrig@…  |      Owner:  Greg Couch
              Type:  defect         |     Status:  assigned
          Priority:  normal         |  Milestone:
         Component:  Input/Output   |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+------------------------
Comment (by Greg Couch):

 Let's be clear, this isn't a problem with a small molecule CIF file.  It
 is a problem with mmCIF file that has no atoms and is just a chemical
 component template.  The workaround is to use "open ccd:PIM" which fetches
 the template (may already be cached on the local disk).  That converts the
 CCD template into a residue.  For now, if you really want to download the
 file, instead of having ChimeraX download it for you, you could put the
 downloaded file in the $HOME/Downloads/ChimeraX/CCD/ directory.  Then use
 "open ccd:PIM". "open PIM from ccd" also works.

 When this bug is fixed, "open PIM.cif format ccd" will also work.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19464#comment:3>
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