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Hi Elaine,</div>
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Rather than measure the distance atom by atom, I constructed the following command. Again, I have two chains, and I want to limit the search just to specific atoms affiliated with those residues. The residues I listed are hydrophobic molecules that are interacting
at two hydrophobic interfaces defined by the "mlp" command. The atoms refer to those pointing at the second interface.</div>
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Here is the command I created, and the error associated with it.</div>
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<span class="ContentPasted0" style="font-size: 12pt; color: black; font-family: Calibri, Helvetica, sans-serif;">contacts /b:77,81,84@CA1,CA2 /c:76,79,195,109,149,150@CA1,CA2,CH2,CZ2</span><span class="ContentPasted0" style="font-size: 13.5pt; color: black;"><o:p class="ContentPasted0"></o:p></span></p>
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<span style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;">Error message:</span></p>
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<span style="font-family: Calibri, Helvetica, sans-serif;"><b style="color: rgb(220, 20, 60); font-size: medium; text-align: start;">No atoms match given atom specifier</b></span><br>
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<span style="font-family: Calibri, Helvetica, sans-serif; color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0); font-size: medium; text-align: start;">Thanks for the help.</span></span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif; color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0); font-size: medium; text-align: start;">Phil</span></span></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> McClean, Phillip <phillip.mcclean@ndsu.edu><br>
<b>Sent:</b> Tuesday, November 15, 2022 5:25 PM<br>
<b>To:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Distance between two atoms</font>
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Hi Elaine,</div>
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Hi Elaine,</div>
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Well I am having fish tonight 😉. I used your suggestion select the atoms on the screen and then run the pop-up distance command and reading the results in the Log. I am still not fully clear about defining atoms and such after reading the atoms page. I
will keep working on it.</div>
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Thanks for your help.</div>
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Phil</div>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, November 15, 2022 11:03 AM<br>
<b>To:</b> McClean, Phillip <phillip.mcclean@ndsu.edu><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Distance between two atoms</font>
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<div class="x_PlainText">Hi Phil,<br>
There is a "distance" command, use command "help distance" or see the help at our website here:<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html">https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html</a>><br>
<br>
...and many examples of how to specify atoms in the command line here:<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy">https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy</a>><br>
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Why don't you give it a few tries? We need to "teach a man to fish" since we can't tell thousands of users how to write each command they need for their research.<br>
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Or you can just choose the atoms from the screen: first make sure they are displayed so you can actually see them, and then Ctrl-click one, Shift-Ctrl-doubleclick the second one and choose "Distance" from the resulting pop-up menu. This also is described in
the help (Selection Context Menus):<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context">https://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context</a>><br>
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Best,<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>
> On Nov 15, 2022, at 8:30 AM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Hi Everyone,<br>
> <br>
> I have a two chain model. I would like to determine the distance between the CD1 atom of residue 77 in chain B and the CD1 atom of residue Leu 150 in chain C. What would be the proper distance command.<br>
> <br>
> Thanks for the help again.<br>
> <br>
> Phil McClean<br>
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