Hi Elaine, select :CH6 or disp :CH6 work in Chimera as well. Thanks a lot, Marco Il 16/12/2022 18:18, Elaine Meng ha scritto:

Hi Marco, Hmmm, it may be a bug that this residue does not appear in the Select... Residue menu.

However, I can see by looking in the PDB file (or by opening this structure in ChimeraX) that the nonstandard residue name is CH6, so you can

disp :CH6

for example, or do other things to it, e.g. color, select, ...

select :CH6

The residue does appear in the ChimeraX menu Select... Residue, so the bug seems to be specific to Chimera.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Dec 16, 2022, at 8:49 AM, Marco Sette via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear all,

When I fetch a protein with a chromophore (PDB code 2h5q), the chromophore, not a standard one, is missing, and not present in the Select-Residue menu. Is there any way to obtain it?

Thanks,

Marco

-- Dr Marco Sette, PhD. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it Tel.: +39-0672594424 -- Questa email è stata esaminata alla ricerca di virus dal software antivirus Avast. www.avast.com

It does appear in Chimera's Select menu, but among the standard residues, probably where it shouldn't be. --Eric Eric Pettersen UCSF Computer Graphics Lab

On Dec 16, 2022, at 9:18 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi Marco, Hmmm, it may be a bug that this residue does not appear in the Select... Residue menu.

However, I can see by looking in the PDB file (or by opening this structure in ChimeraX) that the nonstandard residue name is CH6, so you can

disp :CH6

for example, or do other things to it, e.g. color, select, ...

select :CH6

The residue does appear in the ChimeraX menu Select... Residue, so the bug seems to be specific to Chimera.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Dec 16, 2022, at 8:49 AM, Marco Sette via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear all,

When I fetch a protein with a chromophore (PDB code 2h5q), the chromophore, not a standard one, is missing, and not present in the Select-Residue menu. Is there any way to obtain it?

Thanks,

Marco

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users