[Chimera-users] helices

A G Szabo agszabo at bell.net
Thu Nov 19 07:59:16 PST 2015


Elaine

Thanks will try it.

art

-----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
-----
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 <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
large.
> 
> 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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