Replace RCSB ligand-expo URL which is being retired.

[Tom Goddard]

The Ligand Expo RCSB site is being retired and the following URL will cease to work at some point

​http://ligand-expo.rcsb.org/

The new URL to fetch a ligand .cif file is

​https://files.rcsb.org/ligands/download/HEM.cif

ChimeraX is using this in the mmcif reader in mmcif.pyx _get_template(). This should be fixed for the ChimeraX 1.11 release.

This was reported by Brinda Vallat and Ezra Peisach:

On 11/13/25 9:07 AM, Brinda Vallat wrote:
Hi Tom,

Ezra (cc'd here) has pointed out that there are some references to ligand expo in ChimeraX.

We want to inform you that ligand expo is being shutdown. Please check to make sure that any old references are taken care of.

Please let us know if you have any questions.

Thank you,
Brinda

--
BRINDA VALLAT, Ph.D.
RCSB PDB

---

From: Ezra Peisach
Subject: Re: Ligand-expo to be shutdown
Date: November 13, 2025 at 6:47:58 AM PST
To: Brinda Vallat, Tom Goddard

For further details..

I noticed that you have a shared library that references ligand-expo. The centos-7 version of ChimeraX had a python module which performed downloads from there

% strings ./usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/mmcif/mmcif.cpython-311-x86_64-linux-gnu.so | grep ligand-ex
​http://ligand-expo.rcsb.org/

If you are still downloading from ligand-expo, I suggest a changed the the RCSB PDB download API such as:

​https://files.rcsb.org/ligands/download/HEM.cif

Thank you very much,

Ezra Peisach

[Greg Couch]

The problem is that ​https://files.rcsb.org/ligands/download/ doesn't have all of the ligands that are in ligand-expo. For example, ​http://ligand-expo.rcsb.org/reports/S/SER_LL_DHG/SER_LL_DHG.cif used to work. And ​https://files.rcsb.org/ligands/download/SER_LL_DHG.cif doesn't.

ChimeraX's current protocol for using ligand-expo is if the ligand name has an underscore in it. Otherwise it uses ​https://files.wwpdb.org/pub/pdb/refdata/chem_comp/{name[-1]}/{name}/{name}.cif.

This functionality is very important for the ISOLDE extension for ChimeraX.

[Greg Couch]

More examples:

​http://ligand-expo.rcsb.org/reports/S/SER_LSN3_DHG/SER_LSN3_DHG.cif
​http://ligand-expo.rcsb.org/reports/T/THR_LL_DHG1/THR_LL_DHG1.cif
​http://ligand-expo.rcsb.org/reports/S/SER_LEO2_DHG/SER_LEO2_DHG.cif
​http://ligand-expo.rcsb.org/reports/T/THR_LSN3_DHG1/THR_LSN3_DHG1.cif
​http://ligand-expo.rcsb.org/reports/S/SER_LFZW_DHG/SER_LFZW_DHG.cif
​http://ligand-expo.rcsb.org/reports/T/THR_LEO2_DHG1/THR_LEO2_DHG1.cif
​http://ligand-expo.rcsb.org/reports/T/THR_LFZW_DHG1/THR_LFZW_DHG1.cif

[ezra.peisach@…]

I see.  These are from the variant dictionary.   I was not aware that 
ligand-expo was providing an interface to access this data.

Let me get back to you and see if we can come up with a solution.

--Ezra


On 11/13/25 8:09 PM, ChimeraX wrote:
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>

[Tristan Croll]

This shouldn't be a problem for ISOLDE... in response to some prior issues
I've had the aa-variants-v1.cif (along with a "core_components.cif"
containing the most common standard residues) bundled into the distribution
for a while now. They're used by ISOLDE to fill in the blanks on truncated
residues to get them simulation-ready... kept getting bug reports from
people whose firewall settings were blocking the RCSB. From #19367 it looks
like I'll need to update the bundled file, but otherwise everything should
be fine.

On Fri, Nov 14, 2025 at 7:59 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[Greg Couch]

Hi Ezra,

You should be able to use the HTTP User-Agent in your ligand-expo web server logs to see which versions of ChimeraX are still using it. The user agent should look like 'UCSF-ChimeraX/1.11 (Windows 10.0.19045 AMD64)' -- so you can extract the ChimeraX version, the OS, and the CPU architecture.

It would be especially interesting to if there are any requests from recent versions of ChimeraX (so 1.9, 1.10, or 1.10.1), and if so, what entries they are getting.

[Greg Couch]

Hi Ezra and Brinda,

Do you have an update for us? We're about to release a new version of ChimeraX in a few weeks and would like to make any needed changes before the release. The following release of ChimeraX will probably be in June 2026.

-- Greg

[ezra.peisach@…]

I think the best option is to cache/distribute the alternatives file.  
The only update in the last 15 years was one of dictionary compliance - 
there has not been a material change to the files that I am aware of.

-Ezra


On 12/1/25 5:38 PM, ChimeraX wrote:
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[Greg Couch]

An advantage of using ligand-expo is that the rarely used variant templates don't add to the ChimeraX's huge download size. That is also a reason for not including components.cif (and the fact that components.cif is ever increasing in size).

Why not put the individual templates on wwpdb like the other residue templates? Either in ​https://files.wwpdb.org/pub/pdb/refdata/chem_comp/ or maybe a new subdirectory like ​https://files.wwpdb.org/pub/pdb/refdata/chem_comp_variants/.

Did you ever survey how much of a problem this really is with recent versions of ChimeraX? ChimeraX provides a distinctive user agent in its requests that includes the ChimeraX version number.