Hi Elaine,
Thank you for the quick feedback. My problem was that I was using PDB files without the proper mmCIF headers. ChatGPT was helpful in
explaining that non-standard residues can have a designated parental compound, which is defined in the mmCIF header:
loop_
_chem_comp.id
_chem_comp.mon_nstd_parent_comp_id
2MA A
2MG G
Since I had several PDB files where I had done refinement, alignments, scaling and other things, I did not want to go through the trouble
of converting them all to mmCIF. But fortunately, it seems ChimeraX only keeps one definition of monomer non-standard parent compounds, so it was sufficient for me to load one proper .mmCIF downloaded from the PDB so get the mapping correct.
Short story, I just ran “open 7k00 fromDatabase pdb format mmcif” and after that all my modified nucleotides rendered correctly.
Regards,
Daniel
From:
Elaine Meng <meng@cgl.ucsf.edu>
Reply to: chimerax-users <chimerax-users@cgl.ucsf.edu>
Date: Tuesday, 12 May 2026 at 17:32
To: Daniel Larsson <daniel.larsson@icm.uu.se>
Cc: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] nucleotide tube/slab or slab for modified nucleotides
Hi Daniel,
In my test of a recent daily build, 2MA and 2MG in PDB 7k00 are shown as slabs. Maybe you need a newer version of ChimeraX? ChatGPT should always suggest getting a recent version -- then it might have a higher success rate.
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There was a ticket previously to show slabs for more modified bases (#1211) but closed 18 months ago.
Regards,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On May 12, 2026, at 6:59 AM, Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Is it possible to show modified nucleotides as tube/slab or slab? Some common modified residues are recognized as nucleotides, such as PSU, but not e.g. 2MA or 2MG (present in e.g. PDB 7K00)? ChatGPT suggested to rename the residues or redefine the polymer
type, but these tricks do not work.
>
> Regards,
> Daniel
>