[Chimera-users] Wire thickness
Hernando J Sosa
hernando.sosa at einstein.yu.edu
Wed May 10 13:27:39 PDT 2017
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 at einstein.yu.edu
From: Elaine Meng [mailto:meng at 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
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 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 at 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).
>> 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).
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