[chimerax-users] chimeraX questions on representation

[Elaine Meng]

Hi Eddie,
(1) ball scale only applies to ball-and-stick style.  Sphere style shows VDW radii and although you can change these radii, it isn’t recommended because it will affect other things like clash detection, surface display and/or surface-area calculations.  So, use the ball-and-stick style and then use the “size” command to change ball scale, e.g.

size ballScale .5

… that would affect all atoms, although of course it will only be apparent for the atoms that are displayed as ball.  You can also specify subsets of the atoms.  Initial default ballScale is 0.3.  See “size” manpage 
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html>

(2) Yes, there is no way around it.  Changing the representation will change the representation even if the atoms are not displayed, but you can’t tell until you display some of those atoms.  I don’t know why your H’s are disconnected specifically, but it’s almost surely some issue with the input file.

(3) if you mean that you can see faceting on sphere or ball atoms and you want a smoother appearance, you can try using “vr” with “simplify false”, see 
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/device.html#vr>
However, there is a reason that vr automatically simplifies the graphics: to make it more likely that rendering is fast enough to avoid stuttering.  If there is stuttering in VR, it can be very nauseating.

(4)  Just click the mouse-mode icon for zoom (scaling).  The zoom icon looks like two arrows in a diagonal orientation, see <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 15, 2018, at 2:02 PM, Dr. Eddie <eackad at gmail.com> wrote:
> 
> Hi,
> I have a few small n00b questions that would really help me along. 
> 1) How do I change the "ball scale" property in chimeraX using a command for the sphere representation?
> 2) When I do "select protein" (which is represented as a cartoon) it highlights it but clicking on any of the buttons to change the representation does nothing. I need to click first on the show atoms and then I can click on those but many of the H are not connected (for LYS I have two white dots floating above the carbon with no bond to them, but a bond to other C's and it is only for one CH3 group, the other is fine). This is true in all three representations. How do I fix this?
> 3) Can I increase the resolution in VR? 
> 4) After clocking on the label tool with a VIVE controller and using it, how to I change it back to the original mode so I can scale the model (using both triggers)?
> Thank you very much for your help!
> Eddie