Re: [chimerax-users] Ball-and-stick model modification

Hi Volodymyr, Besides "setattr" mentioned by Tristan, there is also a "size" command that is probably friendlier, with options for ball scale and stick radius, e.g.: size #1 ballScale 0.1 stickRadius 0.1 https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html GUI options: In the current version1.3 daily build, bond stick radius is already in the GUI, in the Selection Inspector. E.g. make a selection that includes some bonds, and choose Actions... Inspect or click the magnifying-glass icon in the toolbar Home tab to show the Selection Inspector, and then in that dialog change the menu of what is inspected from Atoms to Bonds, then edit the Radius field to change it for the currently selected bonds. Selection Inspector: https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html Not yet, but soon the Selection Inspector will also have an "Atomic Models" section that will include the ball scale (since there is only one value of that per model). Now in the Atoms you can already edit the radius but in general be careful modifying that VDW radius because it will affect other calculations. If you had used non-chemically reasonable VDW radii, you can change them back to the defaults with the "size" command mentioned above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 21, 2021, at 4:18 AM, Volodymyr Dvornyk via ChimeraX-users wrote:

Thanks a lot! I will try. It would be nice to implement this in the GUI though.

Best,

Volodymyr From: Tristan Croll Sent: Monday, June 21, 2021 14:16 To: ChimeraX-users@cgl.ucsf.edu; Volodymyr Dvornyk Subject: Re: Ball-and-stick model modification

Hi Volodymyr,

You can change the ball diameter with the command:

setattr #1 model ball_scale {scale}

... where scale is a multiplier on the van der Waals radii of the atoms (the default is 0.25). Bond radii can be changed with:

setattr #1 bonds radius {radius}

(default is 0.2). Colors can be set by selecting the atoms to color, then:

color sel {color spec}

... where {color spec} is either a name ("color list" to get the full list of built-in colors), a comma-separated list of 3 (RGB) or 4 (RGBA) numbers on a 0-100 scale, or a built-in specifier like "byhetero" or "bychain". Do "usage color" for a more complete set of options.

Hope this helps!

Tristan From: ChimeraX-users on behalf of Volodymyr Dvornyk via ChimeraX-users Sent: 21 June 2021 11:02 To: ChimeraX-users@cgl.ucsf.edu Subject: [chimerax-users] Ball-and-stick model modification

Hello,

I wonder whether it is possible to modify the ball-and-stick model shape, i.e., change color, ball diameter, stick length, etc. Right now, the only available presentation style is like one in the attachment. Maybe there is some way to modify it but I was unable to find.

Thank you,

Volodymyr

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