[Chimera-users] helices

A G Szabo agszabo at bell.net
Fri Dec 4 09:32:50 PST 2015



So I tried to enlarge the size of the balls in the ball and stick image of
an amino acid


What you see below is the command line 

The  command was highlighted in blue after I hit return. Nothing happened.
So don't know if I have it correct or not.


A part of the image is also shown below. I am trying to change the size of
the balls in the tryptophan amino acid. The molecule in the large spheres is
a maltose. The Trp residue shows it has been selected.


Your assistance will be appreciated


Thank you


Arthur G. Szabo





-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: November-18-15 5:57 PM
To: A G Szabo
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] helices


Hi Arthur,

There isn't anything in the menu to do that, but it can be done with
commands or in the Selection Inspector.  I'll describe one way.


When you show ball-and-stick, the balls are at some fraction of the VDW
radii.  When you show spheres, it is the full VDW radii.  You could change
the VDW radii, but probably a better method is to show ball-and-stick but
change what fraction they are of the VDW radii.  The default is 0.25.  To
change it you could use a command something like:


setattr m ballScale 0.5


That would make ball-and-stick balls half the radius of the spheres.  Of
course, you could try other values and just see what you like.  The "m" is
because this setting is for the whole molecule model; you can't have
different values for different atoms in the same model.  


You can show the command line from the Favorites menu. You can also make
sticks fatter and thinner in a similar way, with stickScale (default 1.0).


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 Nov 18, 2015, at 2:25 PM, A G Szabo < <mailto:agszabo at bell.net>
agszabo at bell.net> wrote:


> Elaine


> But now I have another question that is related to the one I managed 

> to figure out.


> When I highlight an amino acid residue on a structure I know how to 

> visualize the amino acid as a ball and stick structure. I also know 

> how to have the residue shown as spheres.  Except the Spheres are way too


> Is there a  way in which I can reduce the size of the spheres?


> I couldn't find anything obvious in the Tools menu.


> Thank you


> Arthur G. Szabo


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