[Chimera-users] Wire thickness

Hernando J Sosa hernando.sosa at einstein.yu.edu
Wed May 10 13:27:39 PDT 2017

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 at einstein.yu.edu

-----Original Message-----
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

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 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).
> 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.

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