One last one: (5) You can reference all chains with identical sequences to a given chain with the chain “identity” attribute, e.g. to color chain A and all chains with the same sequence as A red: color //identity=“/A” red --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 30, 2025, at 2:00 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Matthias, Current features that may help are:
(1) the chain IDs and descriptions are shown in the Log when you open the structure. If this scrolls away you can show it again later using command "log chains" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#chains>
(2) you can already select directly by this info, e.g. menu: Select... Chains contains entries that are the chain descriptions, e.g.: HEMOGLOBIN (DEOXY) (ALPHA CHAIN)
(3) pausing the cursor over the chain in the graphics window reports the chain description in the status line across the bottom
(4) if you open the Uniprot sequence by clicking its name in the aforementioned table, it loads the sequence with all of its feature annotations, and associates it with all of the corresponding structure chains. See "model information" and "UniProt sequence features" <https://rbvi.ucsf.edu/chimerax/docs/user/modelinfo.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#uniprot>
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 Jan 30, 2025, at 1:45 PM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi again : ) When comparing structures from different sources (such as different PDB depositions, or an Alphafold structure), it is always tedious to figure out which chain belongs to which protein (especially for large structures like spliceosomes) for consistent coloring or alignment. I wondered if it would be technically feasible to use the uniport ID to match a specific chain directly, since the association between chain ID and uniport ID should be present at least in structures from curated databases such as the PDB and Alphafold. So the ambition would be to be able to use ‘colorIF4A3_HUMAN red’ directly, without having to look chain IDs. An added bonus would be to be able to skip the species identifier, in case you have models containing IF4A3_MOUSE and IF4A3_HUMAN, and match both with IF4A3 …. Would be curious to hear your thoughts. Thanks a lot, and best wishes, Matthias
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