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<span style="font-family: Arial, Helvetica, sans-serif;">Volodymyr,</span></div>
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<span style="font-family: Arial, Helvetica, sans-serif;">My SEQCROW bundle has a tool for changing distances between atoms. You can install it by going to Tools -> More Tools...
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<span style="font-family: Arial, Helvetica, sans-serif;">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:</span><br>
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<li><span style="font-family: Arial, Helvetica, sans-serif;">Select any number of bonds or a single pair of atoms</span></li><li><span style="font-family: Arial, Helvetica, sans-serif;">enter a bond length on the tool</span></li><ol style="list-style-type: lower-alpha;">
<li><span style="font-family: Arial, Helvetica, sans-serif;">the "bond length lookup" can help with expected bond lengths for specified elements and bond orders</span></li><li><span style="font-family: Arial, Helvetica, sans-serif;">you can change the elements by clicking one the elements, which opens a periodic table</span></li><li><span style="font-family: Arial, Helvetica, sans-serif;">depending on the elements, SEQCROW might have a speculative bond length for single, aromatic (1.5x), double, or triple bonds</span></li></ol>
<li><span style="font-family: Arial, Helvetica, sans-serif;">choose which side of the bond to move (smaller, larger, or both) to meet the specified bond length</span><br>
</li><li><span style="font-family: Arial, Helvetica, sans-serif;">click "change selected bond lengths" to apply any changes.</span></li><ol style="list-style-type: lower-alpha;">
<li><span style="font-family: Arial, Helvetica, sans-serif;">If you've selected multiple bonds in the same ring system, you might have to click this a few times</span></li></ol>
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<div><span style="font-family: Arial, Helvetica, sans-serif;">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
</span><span style="font-family: Arial, Helvetica, sans-serif;">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.</span><br>
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<div><span style="font-family: Arial, Helvetica, sans-serif;">Best,</span></div>
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<div><span style="font-family: Arial, Helvetica, sans-serif;">Tony</span><br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Volodymyr Dvornyk via ChimeraX-users <chimerax-users@cgl.ucsf.edu><br>
<b>Sent:</b> Monday, June 21, 2021 11:23 AM<br>
<b>To:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Ball-and-stick model modification</font>
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<div class="PlainText">[EXTERNAL SENDER - PROCEED CAUTIOUSLY]<br>
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<br>
Thanks a lot! One more question: how to increase bond length (distance between atoms)?<br>
<br>
Best,<br>
<br>
Volodymyr<br>
<br>
-----Original Message-----<br>
From: Elaine Meng <meng@cgl.ucsf.edu><br>
Sent: Monday, June 21, 2021 17:53<br>
To: Volodymyr Dvornyk <vdvornyk@alfaisal.edu><br>
Cc: Tristan Croll <tic20@cam.ac.uk>; ChimeraX-users@cgl.ucsf.edu<br>
Subject: Re: [chimerax-users] Ball-and-stick model modification<br>
<br>
Hi Volodymyr,<br>
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.:<br>
<br>
size #1 ballScale 0.1 stickRadius 0.1<br>
<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html">https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html</a>><br>
<br>
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.<br>
<br>
Selection Inspector:<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html">https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html</a>><br>
<br>
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.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On Jun 21, 2021, at 4:18 AM, Volodymyr Dvornyk via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
><br>
> Thanks a lot! I will try. It would be nice to implement this in the GUI though.<br>
><br>
> Best,<br>
><br>
> Volodymyr<br>
> From: Tristan Croll <tic20@cam.ac.uk><br>
> Sent: Monday, June 21, 2021 14:16<br>
> To: ChimeraX-users@cgl.ucsf.edu; Volodymyr Dvornyk <vdvornyk@alfaisal.edu><br>
> Subject: Re: Ball-and-stick model modification<br>
><br>
> Hi Volodymyr,<br>
><br>
> You can change the ball diameter with the command:<br>
><br>
> setattr #1 model ball_scale {scale}<br>
><br>
> ... 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:<br>
><br>
> setattr #1 bonds radius {radius}<br>
><br>
> (default is 0.2). Colors can be set by selecting the atoms to color, then:<br>
><br>
> color sel {color spec}<br>
><br>
> ... 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.<br>
><br>
> Hope this helps!<br>
><br>
> Tristan<br>
> From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Volodymyr Dvornyk via ChimeraX-users <chimerax-users@cgl.ucsf.edu><br>
> Sent: 21 June 2021 11:02<br>
> To: ChimeraX-users@cgl.ucsf.edu <ChimeraX-users@cgl.ucsf.edu><br>
> Subject: [chimerax-users] Ball-and-stick model modification<br>
><br>
> Hello,<br>
><br>
> 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.<br>
><br>
> Thank you,<br>
><br>
> Volodymyr<br>
><br>
><br>
><br>
><br>
><br>
><br>
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