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Hi Elaine,</div>
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Yes, I picked up the command info also from the Log. It is a good way to learn; thanks for the tip.</div>
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I had in the past tried to better understand the details in the Atom Specification page. Some I understood, others, not so much. What has always been a puzzle is why a model number is used? I am assuming now that the # symbol is need to distinguish models
when two are loaded in the same session. Make sense? Otherwise, I don't really understand the use of that symbol.</div>
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Phil</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, November 15, 2022 6:06 PM<br>
<b>To:</b> McClean, Phillip <phillip.mcclean@ndsu.edu><br>
<b>Cc:</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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<div class="PlainText">Hi Phil,<br>
When I used the selection context menu approach (pick atoms from screen) then my Log showed this:<br>
<br>
distance /A:310@O4 /A:236@OD1<br>
<br>
The / symbol means chain ID, the : symbol means residue number, and the @ symbol means atom name, as explained 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>
<br>
There are several examples in that page if you scroll down a bit from there.<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 Nov 15, 2022, at 3:25 PM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Hi Elaine,<br>
> <br>
> Hi Elaine,<br>
> <br>
> 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.<br>
> <br>
> Thanks for your help.<br>
> <br>
> Phil<br>
> From: Elaine Meng <meng@cgl.ucsf.edu><br>
> Sent: Tuesday, November 15, 2022 11:03 AM<br>
> To: McClean, Phillip <phillip.mcclean@ndsu.edu><br>
> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
> Subject: Re: [chimerax-users] Distance between two atoms<br>
> <br>
> 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>
> <br>
> 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>
> <br>
> 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>
> <br>
> 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>
<br>
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