Thanks a lot! I will try. It would be nice to implement this in the GUI though. Best, Volodymyr From: Tristan Croll <tic20@cam.ac.uk> Sent: Monday, June 21, 2021 14:16 To: ChimeraX-users@cgl.ucsf.edu; Volodymyr Dvornyk <vdvornyk@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@cgl.ucsf.edu<mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of Volodymyr Dvornyk via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: 21 June 2021 11:02 To: ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> <ChimeraX-users@cgl.ucsf.edu<mailto: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 ________________________________ 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. ________________________________ 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.

Thanks a lot! One more question: how to increase bond length (distance between atoms)? Best, Volodymyr -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, June 21, 2021 17:53 To: Volodymyr Dvornyk <vdvornyk@alfaisal.edu> Cc: Tristan Croll <tic20@cam.ac.uk>; ChimeraX-users@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@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@cam.ac.uk> Sent: Monday, June 21, 2021 14:16 To: ChimeraX-users@cgl.ucsf.edu; Volodymyr Dvornyk <vdvornyk@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@cgl.ucsf.edu> on behalf of Volodymyr Dvornyk via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 21 June 2021 11:02 To: ChimeraX-users@cgl.ucsf.edu <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

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.

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. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

________________________________ 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.

And one more question: is there any option to distinguish double and single bonds in the figure? Thank you! -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, June 21, 2021 17:53 To: Volodymyr Dvornyk <vdvornyk@alfaisal.edu> Cc: Tristan Croll <tic20@cam.ac.uk>; ChimeraX-users@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@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@cam.ac.uk> Sent: Monday, June 21, 2021 14:16 To: ChimeraX-users@cgl.ucsf.edu; Volodymyr Dvornyk <vdvornyk@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@cgl.ucsf.edu> on behalf of Volodymyr Dvornyk via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 21 June 2021 11:02 To: ChimeraX-users@cgl.ucsf.edu <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

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.

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. _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

________________________________ 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.