Dear Leyre, It sounds like the phenix output file does not contain the full sequence information that was in the original structure. Did you close the first sequence window that has the boxed missing residues? If that previous sequence window is still open, you can simply associate the refined structure with the sequence in that window, e.g. in the dialog you get from choosing "Structure... Associations..." from the sequence-window context menu: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context> Or if you already closed that original sequence window, if you re-open the original structure (or any structure that still has the full sequence information), show the sequence for that structure to get it back. Then open your refined structure, and associate it with that sequence. Do not close the original structure until after you associate the refined structure and close the association dialog. In recent daily builds (1.9, newer than the last release), after the refined structure is associated with that sequence, you can put the sequence into that structure's information by choosing "Structure... Update Chain Sequence" from the sequence-window context menu. You would then need to save a PDB or mmCIF file with the new sequence information (main menu: File... Save, or "save" command) so that next time you open that refined structure file, it will have the full sequence when you show the sequence window. save command help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html> 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 Jul 4, 2024, at 12:47 PM, Leyre Marin Arraiza via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear UCSF ChimeraX,

I have a practical question regarding model sequence visualization after real.space.refinement in phenix.

After I worked on my model in ISOLDE and Coot, I deleted some residues that were out of the map density. Then, a dashed line appeared in my model, connecting the gap between the remaining residues (example, ALA97------GLN110). When I visualize the model sequence in ChimeraX, the deleted residues appear boxed with a rectangle, to indicate they are missing in the structure.

Once I get the results back from the phenix real.space.refinement, and I visualize the model sequence in ChimeraX again, the deleted residues do not appear boxed anymore, but they are gone instead from the visualized sequence, keeping their corresponding numbers but not showing a boxed gap (in the example I mentioned they jump from 97 to 110 directly).

I would like to keep the deleted residues boxed in the sequence when I visualize it. Is that possible?

Hope I am explaining myself. Thanks and best regards, Leyre

Leyre Marin Arraiza PhD fellow

University of Copenhagen Novo Nordisk Foundation Center for Protein Research Taylor Group Blegdamsvej 3B, Building 6, 6-1-10 2200 København N

leyre.arraiza@cpr.ku.dk

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