Hi Eddie,

Here’s a bit more detail on your VR questions 3 and 4. If you open a big atomic model, say 100,000 atoms then when you turn on VR in ChimeraX it will make the atom spheres look very faceted, maybe showing them like icosahedrons. This is because the graphics can’t render fast enough for VR. VR needs 90 frames per second in 2 eyes, so the equivalent of 180 frames per second. On a conventional display you can get by with 10 frames per second so ChimeraX shows smoother spheres on a conventional display. The vr command option Elaine mentioned “vr on simplify false” would use the smoother spheres but then the VR will flicker badly even on the fastest graphics card available (e.g. a 2080 Ti). But you can perhaps make the spheres a bit smoother using the command “graphics atomTriangles 40” which will use 40 triangles to approximate each atom sphere.

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html

Using the command “graphics” with no options will tell you how many triangles are currently being used per sphere.

For your question about how to change the Vive hand-controller back to moving models, you should click on the rotate or translate mouse mode icons with the hand controller. These are the two half-circle arrows or the 4 arrows forming a plus sign, the second and third icons in the mouse modes panel. The zoom icon Elaine suggested won’t get you back to moving models an zooming using two hand-controllers — that is a different mode that lets you zoom with one hand by holding the button and raising and lowering the controller, not so useful. Instead of switching back and forth to move/zoom what I suggest is that when you switch int label mode, click with your thumb on the hand-controller trackpad — don’t click with your index finger. This assigns the trackpad click to add a label, and then the index finger trigger click continues to move / zoom models. You can also reassign the grip buttons on the Vive controllers — so each Vive controller can have 3 different modes assigned to trigger, grip, and trackpad a total of 6 modes for the 2 hand controllers.

Tom

On Oct 15, 2018, at 8:35 PM, Elaine Meng meng@cgl.ucsf.edu wrote:

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

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

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On Oct 15, 2018, at 2:02 PM, Dr. Eddie eackad@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

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