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<p class="MsoNormal">Hi Eric,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you so much for your input. I think I found the issue:</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The script works when disabling gui if I use chimera-console to execute it from terminal.</p>
<p class="MsoNormal">So, the following works: ChimeraX-console --nogui --script myscript.py</p>
<p class="MsoNormal">And this one does not work: ChimeraX --nogui -script myscript.py
</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Is this how it is supposed to be?</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Shubham.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">
Mail</a> for Windows</p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="border:none;padding:0in"><b>From: </b><a href="mailto:pett@cgl.ucsf.edu">Eric Pettersen</a><br>
<b>Sent: </b>Wednesday, May 11, 2022 22:44<br>
<b>To: </b><a href="mailto:sdramgoolam@uwaterloo.ca">Shubham Devesh Ramgoolam</a><br>
<b>Cc: </b><a href="mailto:chimerax-users@cgl.ucsf.edu">ChimeraX Users Help</a><br>
<b>Subject: </b>Re: [chimerax-users] no gui mode and redirecting output of some commands</p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Shubham,<o:p></o:p></p>
<div>
<p class="MsoNormal">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.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">--Eric<o:p></o:p></p>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On May 10, 2022, at 10:19 PM, Shubham Devesh Ramgoolam via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">Hi Eric,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Thank you for your reply.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">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).<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">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.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Here is my script:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">from chimerax.core.commands import run<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">from chimerax.atomic import selected_residues<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">run(session, "open C:\\Users\\Shubham\\Desktop\\PDB_Script\\1ebt.pdb") <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">run(session, "sel aromatic & protein")<span class="apple-converted-space"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">with open("C:\\Users\\Shubham\\Desktop\\arom_list.txt", "w") as f:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> for r in selected_residues(session):<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> print(r,file=f)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">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).<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Here is my script for that:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">from chimerax.core.commands import run<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">run(session, "open C:\\Users\\Shubham\\Desktop\\PDB_Script\\1ebt.pdb") <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">run (session, 'define centroid /A:14 & aromatic-ring radius 0.3 color yellow mass false name C1')<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">run (session, 'define centroid /A:21 & aromatic-ring radius 0.3 color yellow mass false name C2')<o:p></o:p></p>
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<div>
<p class="MsoNormal">file = open('C:\\Users\\Shubham\\Desktop\\distance.txt', 'w+')<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">dist = run(session, 'distance @c1 @c2')<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">file.write(str(dist))<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">file.close()<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Regards,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Shubham<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Sent from<span class="apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a><span class="apple-converted-space"> </span>for Windows<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<div>
<p class="MsoNormal"><b>From:<span class="apple-converted-space"> </span></b><a href="mailto:pett@cgl.ucsf.edu">Eric Pettersen</a><br>
<b>Sent:<span class="apple-converted-space"> </span></b>Tuesday, May 10, 2022 22:00<br>
<b>To:<span class="apple-converted-space"> </span></b><a href="mailto:sdramgoolam@uwaterloo.ca">Shubham Devesh Ramgoolam</a><br>
<b>Cc:<span class="apple-converted-space"> </span></b><a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a><br>
<b>Subject:<span class="apple-converted-space"> </span></b>Re: [chimerax-users] no gui mode and redirecting output of some commands<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Hi Shubham,<o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal">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.<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Replace:<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">run(session, "info residue sel")<br>
run(session, "log save aromatic_list.html")<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">with:<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">from chimerax.atomic import selected_residues<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">with open("where-I-want-to-save.txt", "w") as f:<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">for r in selected_residues(session):<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">print(r, file=f)<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">You can do similar things with distances and angles because the commands return the distance/angle values,<span class="apple-converted-space"> </span><i>e.g.</i>:<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">d = run(session, "distance<span class="apple-converted-space"> </span><i>atom1 atom2</i>")<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><i>write/append d to a file</i><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal">--Eric<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Eric Pettersen<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">UCSF Computer Graphics Lab<o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<p class="MsoNormal">On May 10, 2022, at 3:29 AM, Shubham Devesh Ramgoolam via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal">Hi,<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">I hope you are doing well.<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">I have a python script (myscript.py) as follows:<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">from chimerax.core.commands import run<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">import os<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">os.chdir("C:\\Users\\Shubham\\Desktop")<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">run(session, "open C:\\Users\\Shubham\\Desktop\\PDB_Script\\1ebt.pdb") # location of my pdb file<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">run(session, "sel aromatic & protein") <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">run(session, "log clear")<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">run (session, "info residue sel")<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">run(session, "log save aromatic_list.html")<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">I am using the following prompt for calling chimerax from command prompt:<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Gui enabled: chimerax --script C:\\Users\\Shubham\\Desktop\\myscript.py<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Gui disabled: chimerax --nogui --script C:\\Users\\Shubham\\Desktop\\myscript.py<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">With gui mode enabled, the html file, aromatic_list.html, is created.<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">However, when disabling gui, nothing is created.<span class="apple-converted-space"> </span><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
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<div>
<p class="MsoNormal">I suspect this is because I am relying on the log which may not be functional when gui is disabled?<o:p></o:p></p>
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<div>
<div>
<p class="MsoNormal">Is there a way of redirecting the output of certain commands (e.g info, distance, angle) to a desired text file when disabling gui?<o:p></o:p></p>
</div>
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<div>
<div>
<p class="MsoNormal">I tried with sys.stdout but it did not work (empty text files were created.).<o:p></o:p></p>
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<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Regards,<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Shubham<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Sent from<span class="apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a><span class="apple-converted-space"> </span>for Windows<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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