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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