[Chimera-users] atom display radius

A G Szabo agszabo at bell.net
Tue May 10 08:59:40 PDT 2016


Elaine 

Thank you will try that

ags

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: May-10-16 11:51 AM
To: A G Szabo
Cc: chimera-users at cgl.ucsf.edu
Subject: atom display radius

Hi Arthur,
You can only change “ball scale” for the whole model, and the “m” in the command is necessary.  However, this will only affect the atoms that are shown as balls.  If other atoms are shown only as sticks and/or as spheres, it will not change how they look.   So to change size of any ball atoms, use something like:

setattr m ballScale 0.5

… which would affect all models, although you might only have one model open anyway.   You could also put a “sel” at the end to mean only the model(s) containing your selection, but it would still apply to the whole model.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

But as I said, if the atom is not shown as a ball (ball-and-stick style) but as a sphere, the ball-scale value will not affect it.  An alternative approach is to actually change the VDW radius of the atom.  You have to be very careful with this since it will generally affect any later calculations of molecular surface, H-bonds, or contacts.  To change VDW radius, you could select the atom(s) and then use a command something like

vdwdef  +0.2  sel

… to increase the VDW radius by 0.2 angstroms of the selected atom(s) only.  This will affect the appearance of sphere and ball (except the amount of change will be scaled by ballscale, since the visible radius of the ball = ballscale X VDW radius), but it will not affect atoms in stick mode.

See manual page:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html>

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 9, 2016, at 6:28 PM, A G Szabo <agszabo at bell.net> wrote:
> 
> I am trying to make the sphere of an ion in an active site larger than what appears in the structure.
> I asked a similar question back in December, and on checking my notes 
> I tried to use the command
> 
> setattr ballScale 0.5
> 
> I first selected the ion using control<click). The ion was selected. I then tried the command line as I show it above.
> Nothing appeared to happen.
> Indeed I tried to do the same for an atom of a residue that I had selected using control <click> again nothing.
> 
> I must have forgotten something.
> A message from Elaine suggested that I use
> 
> setattr m ballScale 0.5
> Am I supposed to select the residue and leave out the m?
> Thanks for your patience.
> Arthur Szabo





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