Hi Hernando, I used the ca_and_sidechains alias in this script (you should be able to get the individual commands from that). https://github.com/olibclarke/chimera-trimmings/blob/master/chimera_aliases.... Cheers Oli
Dear Chimera How do you set the thickness of the backbone and side chains independently to produce figures like the ones below (sorry I hijacked the picture used in blurred-display discussion).
Thanks
H.
Hi Hernando, To summarize for you and others: first you have to show sticks instead of wires, then set the stick radii. In Chimera, the individual bond “radius” (default 0.2 Angstroms) is multiplied by molecule-model “stickScale” (default 1.0) to give the stick radius. You can change these attributes in the Selection Inspector (opened with green magnifying glass after making a selection) or with the “setattr” command. Since changing stickScale would change it for the whole model, you instead want to specify the bond “radius” attribute separately for the backbone and non-backbone bonds, for example: setattr b radius 0.1 protein setattr b radius 0.25 @n,ca, c,o … substituting whatever radius values you really wanted. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 10, 2017, at 8:06 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Hernando, I used the ca_and_sidechains alias in this script (you should be able to get the individual commands from that).
https://github.com/olibclarke/chimera-trimmings/blob/master/chimera_aliases....
Cheers Oli
Dear Chimera How do you set the thickness of the backbone and side chains independently to produce figures like the ones below (sorry I hijacked the picture used in blurred-display discussion). Thanks H.
Thanks Elaine!. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa@einstein.yu.edu -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Wednesday, May 10, 2017 12:38 PM To: Hernando J Sosa Cc: UCSF Chimera Mailing List Subject: Re: [Chimera-users] Wire thickness Hi Hernando, To summarize for you and others: first you have to show sticks instead of wires, then set the stick radii. In Chimera, the individual bond “radius” (default 0.2 Angstroms) is multiplied by molecule-model “stickScale” (default 1.0) to give the stick radius. You can change these attributes in the Selection Inspector (opened with green magnifying glass after making a selection) or with the “setattr” command. Since changing stickScale would change it for the whole model, you instead want to specify the bond “radius” attribute separately for the backbone and non-backbone bonds, for example: setattr b radius 0.1 protein setattr b radius 0.25 @n,ca, c,o … substituting whatever radius values you really wanted. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 10, 2017, at 8:06 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi Hernando, I used the ca_and_sidechains alias in this script (you should be able to get the individual commands from that).
https://github.com/olibclarke/chimera-trimmings/blob/master/chimera_al iases.com
Cheers Oli
Dear Chimera How do you set the thickness of the backbone and side chains independently to produce figures like the ones below (sorry I hijacked the picture used in blurred-display discussion). Thanks H.
participants (3)
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Elaine Meng -
Hernando J Sosa -
Oliver Clarke