Select coloured residues with Chimera
Hello, my name is Javier and I am a Bioinformatics PhD student in Dundee. I am using UCSF Chimera v1.14 and I am trying to select residues according to the colour they are coloured in, using the following command for blue-coloured residues for example: "sel @/color=blue". This works just fine, however, I struggle when using other colours such as "medium blue" or "dark green". "sel @/color=darkgreen" does not work. It looks like all colours with a single word name work fine, but 2-word name colours do not. Moreover, I can colour residues using RGB codes, such as "col #da70d6 sel" to colour selected residues in orchid. Nevertheless, "sel @/color=#da70d6" does not work. "sel @/color=orchid" works, though. So, is there a way that I can use two-word named colours when selecting by colours, and also, use RGB codes or other colouring codes to select coloured residues? Many thanks, Javier The University of Dundee is a registered Scottish Charity, No: SC015096
Hi Javier, I know it's counterintuitive, but "dark green" and "darkgreen" are not exactly the same color. Chimera has a builtin list of color names it knows about, which includes dark green (but not darkgreen). If you use a color name not in its builtin list, it falls back to system color names, which in this case includes darkgreen, but darkgreen is slightly different from dark green -- though visually they probably look identical. Therefore you need to use this syntax to select dark green: sel @/color="dark green" As for the color hex codes, the atom-selection syntax does not handle hex codes, only color names. You can work around this by defining an equivalent color name, e.g.: colordef testcol #da70d6 sel @/color=testcol --Eric Eric Pettersen UCSF Computer Graphics Lab
On Oct 13, 2021, at 3:13 AM, Javier Sanchez Utges (PG Research) via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello, my name is Javier and I am a Bioinformatics PhD student in Dundee. I am using UCSF Chimera v1.14 and I am trying to select residues according to the colour they are coloured in, using the following command for blue-coloured residues for example: “sel @/color=blue”. This works just fine, however, I struggle when using other colours such as “medium blue” or “dark green”. “sel @/color=darkgreen” does not work. It looks like all colours with a single word name work fine, but 2-word name colours do not. Moreover, I can colour residues using RGB codes, such as “col #da70d6 sel” to colour selected residues in orchid. Nevertheless, “sel @/color=#da70d6” does not work. “sel @/color=orchid” works, though. So, is there a way that I can use two-word named colours when selecting by colours, and also, use RGB codes or other colouring codes to select coloured residues?
Many thanks,
Javier
The University of Dundee is a registered Scottish Charity, No: SC015096_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
participants (2)
-
Eric Pettersen -
Javier Sanchez Utges (PG Research)