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

[Anthony James Schaefer]

Volodymyr,

My SEQCROW bundle has a tool for changing distances between atoms. You can install it by going to Tools -> More Tools...

After installing SEQCROW, the tool will be under Tools -> Structure Editing -> Bond Editor. There's five tabs on the tool, the last of which is for bond lengths. To use the tool:

  1.  Select any number of bonds or a single pair of atoms
  2.  enter a bond length on the tool
     *   the "bond length lookup" can help with expected bond lengths for specified elements and bond orders
     *   you can change the elements by clicking one the elements, which opens a periodic table
     *   depending on the elements, SEQCROW might have a speculative bond length for single, aromatic (1.5x), double, or triple bonds
  3.  choose which side of the bond to move (smaller, larger, or both) to meet the specified bond length
  4.  click "change selected bond lengths" to apply any changes.
     *   If you've selected multiple bonds in the same ring system, you might have to click this a few times

ChimeraX also has a "move atoms" mouse mode, which can be activated on the "right mouse" tab of ChimeraX's toolbar. You can add a distance label to a pair of atoms using the "distance" mouse mode (on the same tab) and right-clicking on two atoms. Then select all atoms on one side of the bond and activate the "move atoms" mouse mode. Right-clicking and dragging will move the selected atoms, so you can effectively change the bond length.

Best,

Tony
________________________________
From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of Volodymyr Dvornyk via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
Sent: Monday, June 21, 2021 11:23 AM
To: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Ball-and-stick model modification

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


Thanks a lot! One more question: how to increase bond length (distance between atoms)?

Best,

Volodymyr

-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Monday, June 21, 2021 17:53
To: Volodymyr Dvornyk <vdvornyk at alfaisal.edu>
Cc: Tristan Croll <tic20 at cam.ac.uk>; ChimeraX-users at cgl.ucsf.edu
Subject: 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 <chimerax-users at cgl.ucsf.edu> wrote:
>
> Thanks a lot! I will try. It would be nice to implement this in the GUI though.
>
> Best,
>
> Volodymyr
> From: Tristan Croll <tic20 at cam.ac.uk>
> Sent: Monday, June 21, 2021 14:16
> To: ChimeraX-users at cgl.ucsf.edu; Volodymyr Dvornyk <vdvornyk at alfaisal.edu>
> 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 <chimerax-users-bounces at cgl.ucsf.edu> on behalf of Volodymyr Dvornyk via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
> Sent: 21 June 2021 11:02
> To: ChimeraX-users at cgl.ucsf.edu <ChimeraX-users at 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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>
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DISCLAIMER: This electronic mail transmission contains confidential information intended only for the person(s) named. Any use, distribution, copying or disclosure by any other person is strictly prohibited. If you received this transmission in error, please notify the sender by reply e-mail and then destroy the message. Opinions, conclusions, and other information in this message that do not relate to the official business of Alfaisal University shall understand to be neither given nor endorsed by Alfaisal University. The contents of any attachment to this e-mail may contain software viruses, which could damage your own computer system. While “Alfaisal University” has taken every reasonable precaution to minimize this risk, we cannot accept liability for any damage which you sustain as a result of software viruses. You should carry out your own virus checks before opening the attachment.

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