Cannot specify chain ID using /B:300 notation in .defattr file
Dear All, I can make .defattr files that work well for render-by-attribute, if I specify residues only as :arg or :206 (examples). However if I want to specify a particular residue in a particular chain (e.g. /A:206), I can load a .defattr file with no error, but the attribute is not found by the render-by-attribute or select-by-attribute capabilities. (I did not attempt the retired :206.A notation. Maybe I should ?) Has anyone gotten chain-specific resIDs to work in a .defattr file please? Thank you •—•—•—•—•—•—•—•—•—•—•—•—• A.-F. Miller, Ph. D. (she/elle/sie) Gill Eminent Professor Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836 https://millerlablive.wordpress.com/
Hi Anne-Frances, This works fine in my tests. Did you make sure the file format is correct (contains tabs)? <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html> See attached, assigns attribute "blah" to residues /A:1, /A:2, /A:3 You can also save an attribute file with some existing residue attribute to get an example of the proper format, e.g. save phi.defattr attr r:phi <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> I hope this helps, 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 Feb 27, 2026, at 5:18 AM, Anne-Frances Miller via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear All,
I can make .defattr files that work well for render-by-attribute, if I specify residues only as :arg or :206 (examples). However if I want to specify a particular residue in a particular chain (e.g. /A:206), I can load a .defattr file with no error, but the attribute is not found by the render-by-attribute or select-by-attribute capabilities.
(I did not attempt the retired :206.A notation. Maybe I should ?)
Has anyone gotten chain-specific resIDs to work in a .defattr file please?
Thank you •—•—•—•—•—•—•—•—•—•—•—•—• A.-F. Miller, Ph. D. (she/elle/sie) Gill Eminent Professor Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836
Thank ou very much Elaine, I will take this up again over the weekend. In the end, I got a figure made for my collaborators by renumbering one chain so that each residue number was only used once. However I greatly appreciate your leaning in so quickly, since it will be much easier to not have to renumber every time I want to do this. Anne-Frances •—•—•—•—•—•—•—•—•—•—•—•—• A.-F. Miller, Ph. D. (she/elle/sie) Gill Eminent Professor Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836 https://millerlablive.wordpress.com/
On Feb 27, 2026, at 12:19, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Anne-Frances, This works fine in my tests. Did you make sure the file format is correct (contains tabs)? <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html>
See attached, assigns attribute "blah" to residues /A:1, /A:2, /A:3
You can also save an attribute file with some existing residue attribute to get an example of the proper format, e.g.
save phi.defattr attr r:phi
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes>
I hope this helps, 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
<blah.defattr>
On Feb 27, 2026, at 5:18 AM, Anne-Frances Miller via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear All,
I can make .defattr files that work well for render-by-attribute, if I specify residues only as :arg or :206 (examples). However if I want to specify a particular residue in a particular chain (e.g. /A:206), I can load a .defattr file with no error, but the attribute is not found by the render-by-attribute or select-by-attribute capabilities.
(I did not attempt the retired :206.A notation. Maybe I should ?)
Has anyone gotten chain-specific resIDs to work in a .defattr file please?
Thank you •—•—•—•—•—•—•—•—•—•—•—•—• A.-F. Miller, Ph. D. (she/elle/sie) Gill Eminent Professor Distinguished Prof. of Arts and Sciences Professor of Chemistry University of Kentucky https://uky.zoom.us/j/3250841836
participants (2)
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Anne-Frances Miller -
Elaine Meng