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<p>Dear Elaine,</p>
<p><br>
</p>
<p>Yes, it helped! Thanks a lot for your fast and accurate answer :) </p>
<p><br>
</p>
<p>I will keep an eye on the two links you shared with me. </p>
<p><br>
</p>
<p>Best regards,</p>
<p>Iva</p>
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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> Wednesday, April 6, 2022 5:22:17 PM<br>
<b>To:</b> Lucic, Iva<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] Creating distances using the command line</font>
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<div class="PlainText">Hi Iva,<br>
You almost had it. There is no dash ("-") and no spaces in the specification of each atom, so could be something like<br>
<br>
distance #1:347.A@ca #1:323.A@ca<br>
<br>
...if they are really in model #1. Or if there is only one model open anyway, you don't have to give the model number:<br>
<br>
distance :347.A@ca :323.A@ca<br>
<br>
You can see what number your model is in the Model Panel (open from Favorites menu). They start with #0 so maybe your model is #0, not #1.<br>
<br>
The "distance" help page has a few example commands (you can also show this page with command "help distance"):<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html</a>><br>
<br>
...and there are many more example atom specifications in the atom-spec help:<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html</a>><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>
> On Apr 6, 2022, at 7:25 AM, Lucic, Iva via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Hello,<br>
> <br>
> I would like to measure distances between atoms in a structure by using the command line, and not manually by clicking on the atoms and then clicking on "create" button in the Structure Measurements tool.<br>
> <br>
> I would like to map many distances on the same structure (I performed a crosslinking experiments, so I would now like to map the crosslinks on the structure of my protein of interest).<br>
> <br>
> I tried something like distance #1 :347.A@ca - :323.A@ca and similar variations, hoping that I could get the distance between CA atoms of residues 347 and 323 of chain A (there are 12 chains in my protein) from model 1. But I couldn't find a good combination
of commands to give me a distance.<br>
> <br>
> I would highly appreciate any advice. Otherwise, I would have to map manually over 20 crosslinks for each chain...
<br>
> <br>
> Thank you in advance,<br>
> Iva<br>
<br>
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