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<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Hi Tom,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Thanks a lot, this works
</span><span lang="EN-US" style="font-family:"Apple Color Emoji";mso-fareast-language:EN-US">😊</span><span lang="EN-US" style="mso-fareast-language:EN-US"> I originally had tried that, but put the $file at the beginning of the file name, which created output
files named “$file_1.pdb”, “$file_2.pdb”and so forth. Is there a restriction to where in the file name the $file can be, or had I just messed up things somehow?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Thanks again for the amazing support,
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Matthias<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Tom Goddard <goddard@sonic.net><br>
<b>Date: </b>Wednesday, 18. August 2021 at 18:51<br>
<b>To: </b>"Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at><br>
<b>Cc: </b>ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject: </b>Re: [chimerax-users] Automated Fitting of models into maps and saving fits with a correlation score > X<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Matthias,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">When opening a script with the forEachFile option you can use $file in the script which will be replaced by the file basename. So in your script use<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">fitsearch #2 in #1 resolution 20 search 1000 cutoff 0.9 save Tomo_fitted_$file_%d.pdb<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">This is described in the forEachFile documentation<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile">https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Tom<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Aug 18, 2021, at 7:57 AM, Vorländer,Matthias Kopano <<a href="mailto:matthias.vorlaender@imp.ac.at">matthias.vorlaender@imp.ac.at</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Dear Tom,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Thank you again for the code for saving PDBs above a certain correlation score sing the fitmap command! I am now trying do use this on a large number of input volumes, and it’s working well except that I have a problem
with naming the saved PDBs. So, my approach is the following:</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<li class="MsoListParagraph" style="margin-top:0cm;margin-bottom:0cm;mso-list:l0 level1 lfo1">
<span lang="EN-US">Open ChimeraX_Daily in no-gui mode</span><o:p></o:p></li><li class="MsoListParagraph" style="margin-top:0cm;margin-bottom:0cm;mso-list:l0 level1 lfo1">
<span lang="EN-US">Type “</span><span lang="EN-US" style="font-family:"Courier New"">open FitPDBinVolume.cxc foreach *.mrc”</span><o:p></o:p></li></ul>
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<p class="MsoNormal"><span lang="EN-US">The script<span class="apple-converted-space"> </span></span><span lang="EN-US" style="font-family:Courier">FitPDBinVolume.cxc<span class="apple-converted-space"> </span></span><span lang="EN-US">is very simple and looks
like this:</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt;font-family:"Courier New"">open 7apk</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt;font-family:"Courier New"">open /Volumes/matthias.vorlaender/Scripts/Chimera/fit_search.py</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt;font-family:"Courier New"">fitsearch #2 in #1 resolution 20 search 1000 cutoff 0.9 save /Volumes/plaschka/shared/data/em/Krios/20210616_endoTHO_tomo/Visualisation/mapping_back_using_imod/test/Tomo_fitted_%d.pdb</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt;font-family:"Courier New""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">What I would like to achieve is that the fitted PDBs are saved with a base name that matches that of the opened .mrc. Is there an easy way to do that?</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Thanks a lot in advance,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Best,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Matthias</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Courier New""> </span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt">From:<span class="apple-converted-space"> </span></span></b><span style="font-size:12.0pt">ChimeraX-users <<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu">chimerax-users-bounces@cgl.ucsf.edu</a>> on
behalf of "Vorländer,Matthias Kopano via ChimeraX-users" <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>><br>
<b>Reply to:<span class="apple-converted-space"> </span></b>"Vorländer,Matthias Kopano" <<a href="mailto:matthias.vorlaender@imp.ac.at">matthias.vorlaender@imp.ac.at</a>><br>
<b>Date:<span class="apple-converted-space"> </span></b>Tuesday, 27. July 2021 at 07:40<br>
<b>To:<span class="apple-converted-space"> </span></b>Tom Goddard <<a href="mailto:goddard@sonic.net">goddard@sonic.net</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>" <<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] Automated Fitting of models into maps and saving fits with a correlation score > X</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Hi Tom,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif">Thanks so much, that's amazing!</span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif">To be clear, I am not searching tomograms, I am searching artificial tomograms that contain perfect "molmaps" of my protein of interest, so they are free of noise.
Trying this in Chimera gave very good fits when asking for for enough initial placement.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Thanks a lot for your help,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Best, </span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif">Matthias </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Holen Sie sich<span class="apple-converted-space"> </span><a href="https://aka.ms/AAb9ysg">Outlook für Android</a></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b>From:</b><span class="apple-converted-space"> </span>Tom Goddard <<a href="mailto:goddard@sonic.net">goddard@sonic.net</a>><br>
<b>Sent:</b><span class="apple-converted-space"> </span>Tuesday, July 27, 2021 12:15:13 AM<br>
<b>To:</b><span class="apple-converted-space"> </span>Vorländer,Matthias Kopano <<a href="mailto:matthias.vorlaender@imp.ac.at">matthias.vorlaender@imp.ac.at</a>><br>
<b>Cc:</b><span class="apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a><span class="apple-converted-space"> </span><<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [chimerax-users] Automated Fitting of models into maps and saving fits with a correlation score > X<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi Matthias,<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> You can run ChimeraX command scripts or Python scripts without a GUI, just start it at the shell with the "--nogui" option, for example<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">chimerax --nogui mycommands.cxc<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I made some example Python code that runs fitmap search and saves PDB files for each unique fit with correlation over 0.9.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><a href="https://rbvi.github.io/chimerax-recipes/fit_search/fit_search.html">https://rbvi.github.io/chimerax-recipes/fit_search/fit_search.html</a><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I don't expect this to be a good way to search tomograms. It will be very inefficient. Template matching code designed for that problem is likely to work much better. Such code usually uses Fourier space methods to search all translations
at once, so it can be much faster and more thorough. Even with that optimization it takes a long time to do the rotational search.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> Tom<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Example search of monomers in 14-mer GroEL.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><img border="0" width="300" height="334" style="width:3.125in;height:3.4791in" id="x_F2832E31-47FB-4539-A4DD-7042EDD07572" src="cid:image001.png@01D7946E.4B028A10"><o:p></o:p></p>
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<o:p></o:p></p>
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<p class="MsoNormal">On Jul 25, 2021, at 9:05 AM, Vorländer,Matthias Kopano via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Dear all,<span class="xapple-converted-space"> </span></span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">I have a set of 100 “artificial” tomograms, each containing approx 100 copies of a simulated density map of my protein of interest. I would like to fit each tomogram with the PDB of my POI, and save copies for all fits
with a correlation score > 90%. Using the fitmap command in Chimera and then manually selecting the fits that meet the criterium works, but takes quiet a long time for a larger amount of data. I wonder if this could be automated, and if somehow would be able
me to put together a script (is it possible to execute such tasks in a non-gui way, by submitting it to a cluster so that it could be parallelized?).</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Thanks a lot in advance,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Best,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Matthias</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">_______________________________________________<br>
ChimeraX-users mailing list<br>
</span><a href="mailto:ChimeraX-users@cgl.ucsf.edu"><span style="font-size:9.0pt;font-family:Helvetica">ChimeraX-users@cgl.ucsf.edu</span></a><span style="font-size:9.0pt;font-family:Helvetica"><br>
Manage subscription:<br>
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