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<div>Ok. Thanks again for the help Eric.</div>
<div><br>
</div>
<div>Shubham</div>
<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> May 12, 2022 9:22 PM<br>
<b>To:</b> Shubham Devesh Ramgoolam <sdramgoolam@uwaterloo.ca><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] no gui mode and redirecting output of some commands</font>
<div> </div>
</div>
<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Shubham,
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>I’m not the Windows expert on the team but I believe that is correct. Windows enforces a distinction between “command line” and “graphical user interface” programs, so in this case
you should use the command-line version, namely ChimeraX-console.</div>
<div class=""><br class="">
</div>
<div class="">—Eric<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On May 12, 2022, at 3:41 AM, Shubham Devesh Ramgoolam via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
<br class="x_Apple-interchange-newline">
<div class="">
<div class="x_WordSection1" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Hi Eric,</div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
</div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Thank you so much for your input. I think I found the issue:</div>
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</div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
The script works when disabling gui if I use chimera-console to execute it from terminal.</div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
So, the following works: ChimeraX-console --nogui --script myscript.py</div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
And this one does not work: ChimeraX --nogui -script myscript.py</div>
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</div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Is this how it is supposed to be?</div>
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</div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Shubham.</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Sent from<span class="x_Apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986" class="" style="color:blue; text-decoration:underline">Mail</a><span class="x_Apple-converted-space"> </span>for Windows</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif; border:none; padding:0in">
<b class="">From:<span class="x_Apple-converted-space"> </span></b><a href="mailto:pett@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">Eric Pettersen</a><br class="">
<b class="">Sent:<span class="x_Apple-converted-space"> </span></b>Wednesday, May 11, 2022 22:44<br class="">
<b class="">To:<span class="x_Apple-converted-space"> </span></b><a href="mailto:sdramgoolam@uwaterloo.ca" class="" style="color:blue; text-decoration:underline">Shubham Devesh Ramgoolam</a><br class="">
<b class="">Cc:<span class="x_Apple-converted-space"> </span></b><a href="mailto:chimerax-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">ChimeraX Users Help</a><br class="">
<b class="">Subject:<span class="x_Apple-converted-space"> </span></b>Re: [chimerax-users] no gui mode and redirecting output of some commands</div>
</div>
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Hi Shubham,</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
That script works fine on my Mac (with file paths adjusted and using 1EBT from the PDB). It's possible you are getting errors from the script that you are not seeing because output is not going to the terminal/console. Try running the script with the ChimeraX-console
executable instead of the ChimeraX executable and see if that gives you any more information.</div>
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--Eric</div>
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<br class="">
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<blockquote class="" style="margin-top:5pt; margin-bottom:5pt">
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
On May 10, 2022, at 10:19 PM, Shubham Devesh Ramgoolam via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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Hi Eric,</div>
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</div>
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Thank you for your reply.</div>
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I have implemented the change as requested in my python script but I am still facing the same issue: Script works in gui mode but not in nogui mode(no text file made).</div>
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I have tried running the script in the RC build(May 5, 2022), latest production release (Dec 8, 2021), and the daily build (built on May 10, 2022) but to no avail.</div>
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Here is my script:</div>
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</div>
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from chimerax.core.commands import run</div>
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from chimerax.atomic import selected_residues</div>
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</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
run(session, "open C:\\Users\\Shubham\\Desktop\\PDB_Script\\1ebt.pdb") </div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
run(session, "sel aromatic & protein")<span class="x_apple-converted-space"> </span></div>
</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
with open("C:\\Users\\Shubham\\Desktop\\arom_list.txt", "w") as f:</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
for r in selected_residues(session):</div>
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print(r,file=f)</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
I also faced the same issue when writing the output of the command distance (between two centroids) to a text file: Script works in gui mode but not in nogui mode(no text file made).</div>
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Here is my script for that:</div>
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</div>
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from chimerax.core.commands import run</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
run(session, "open C:\\Users\\Shubham\\Desktop\\PDB_Script\\1ebt.pdb") </div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
run (session, 'define centroid /A:14 & aromatic-ring radius 0.3 color yellow mass false name C1')</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
run (session, 'define centroid /A:21 & aromatic-ring radius 0.3 color yellow mass false name C2')</div>
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file = open('C:\\Users\\Shubham\\Desktop\\distance.txt', 'w+')</div>
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dist = run(session, 'distance @c1 @c2')</div>
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file.write(str(dist))</div>
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file.close()</div>
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Regards,</div>
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Shubham</div>
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Sent from<span class="x_apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986" class="" style="color:blue; text-decoration:underline">Mail</a><span class="x_apple-converted-space"> </span>for Windows</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<b class="">From:<span class="x_apple-converted-space"> </span></b><a href="mailto:pett@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">Eric Pettersen</a><br class="">
<b class="">Sent:<span class="x_apple-converted-space"> </span></b>Tuesday, May 10, 2022 22:00<br class="">
<b class="">To:<span class="x_apple-converted-space"> </span></b><a href="mailto:sdramgoolam@uwaterloo.ca" class="" style="color:blue; text-decoration:underline">Shubham Devesh Ramgoolam</a><br class="">
<b class="">Cc:<span class="x_apple-converted-space"> </span></b><a href="mailto:chimerax-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">chimerax-users@cgl.ucsf.edu</a><br class="">
<b class="">Subject:<span class="x_apple-converted-space"> </span></b>Re: [chimerax-users] no gui mode and redirecting output of some commands</div>
</div>
</div>
<div class="">
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Hi Shubham,</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
It seems like a deficiency of the 'info' command that it can't put the information directly into a file. We will look into rectifying that -- and yes, the problem is that the Log does not exist in nogui mode. However, since you are using a Python script for
this (rather than a Chimera command script), you can save the information directly to a file yourself.</div>
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Replace:</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
run(session, "info residue sel")<br class="">
run(session, "log save aromatic_list.html")</div>
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</div>
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with:</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
from chimerax.atomic import selected_residues</div>
</div>
</div>
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<div class="">
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
with open("where-I-want-to-save.txt", "w") as f:</div>
</div>
</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
for r in selected_residues(session):</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
print(r, file=f)</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
You can do similar things with distances and angles because the commands return the distance/angle values,<span class="x_apple-converted-space"> </span><i class="">e.g.</i>:</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
d = run(session, "distance<span class="x_apple-converted-space"> </span><i class="">atom1 atom2</i>")</div>
</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<i class="">write/append d to a file</i></div>
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--Eric</div>
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</div>
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Eric Pettersen</div>
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UCSF Computer Graphics Lab</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
On May 10, 2022, at 3:29 AM, Shubham Devesh Ramgoolam via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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Hi,</div>
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I hope you are doing well.</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
I have a python script (myscript.py) as follows:</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
from chimerax.core.commands import run</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
import os</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
os.chdir("C:\\Users\\Shubham\\Desktop")</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
run(session, "open C:\\Users\\Shubham\\Desktop\\PDB_Script\\1ebt.pdb") # location of my pdb file</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
run(session, "sel aromatic & protein") </div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
run(session, "log clear")</div>
</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
run (session, "info residue sel")</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
run(session, "log save aromatic_list.html")</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
I am using the following prompt for calling chimerax from command prompt:</div>
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Gui enabled: chimerax --script C:\\Users\\Shubham\\Desktop\\myscript.py</div>
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Gui disabled: chimerax --nogui --script C:\\Users\\Shubham\\Desktop\\myscript.py</div>
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With gui mode enabled, the html file, aromatic_list.html, is created.</div>
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However, when disabling gui, nothing is created.<span class="x_apple-converted-space"> </span></div>
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I suspect this is because I am relying on the log which may not be functional when gui is disabled?</div>
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Is there a way of redirecting the output of certain commands (e.g info, distance, angle) to a desired text file when disabling gui?</div>
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I tried with sys.stdout but it did not work (empty text files were created.).</div>
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Regards,</div>
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Shubham</div>
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Sent from<span class="x_apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986" class="" style="color:blue; text-decoration:underline">Mail</a><span class="x_apple-converted-space"> </span>for Windows</div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">_______________________________________________<br class="">
ChimeraX-users mailing list<br class="">
</span><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline"><span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">ChimeraX-users@cgl.ucsf.edu</span></a><span class="" style="font-size:9pt; font-family:Helvetica,sans-serif"><br class="">
Manage subscription:<br class="">
</span><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="" style="color:blue; text-decoration:underline"><span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a></div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">_______________________________________________<br class="">
ChimeraX-users mailing list<br class="">
</span><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline"><span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">ChimeraX-users@cgl.ucsf.edu</span></a><span class="" style="font-size:9pt; font-family:Helvetica,sans-serif"><br class="">
Manage subscription:<br class="">
</span><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="" style="color:blue; text-decoration:underline"><span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a></div>
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<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">ChimeraX-users
mailing list</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline; font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">ChimeraX-users@cgl.ucsf.edu</a><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">Manage
subscription:</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="" style="color:blue; text-decoration:underline; font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div>
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