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Hi Tom,<br>
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Thanks so much, that's amazing!<br>
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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.<br>
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Thanks a lot for your help,</div>
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Best, </div>
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Matthias <br>
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Holen Sie sich <a href="https://aka.ms/AAb9ysg">Outlook für Android</a></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Tuesday, July 27, 2021 12:15:13 AM<br>
<b>To:</b> Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <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</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Matthias,
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<div class=""> You can run ChimeraX command scripts or Python scripts without a GUI, just start it at the shell with the "--nogui" option, for example</div>
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>chimerax --nogui mycommands.cxc</div>
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<div class="">I made some example Python code that runs fitmap search and saves PDB files for each unique fit with correlation over 0.9.<br class="">
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<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span><a href="https://rbvi.github.io/chimerax-recipes/fit_search/fit_search.html" class="">https://rbvi.github.io/chimerax-recipes/fit_search/fit_search.html</a></div>
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<div class="">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.</div>
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<div class=""> Tom</div>
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<div class="">Example search of monomers in 14-mer GroEL.</div>
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<div><img id="x_F2832E31-47FB-4539-A4DD-7042EDD07572" width="300" height="334.906" src="cid:C18A5B82-FCB0-4D8A-ADF0-400431504487" class=""></div>
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<div class="">On Jul 25, 2021, at 9:05 AM, Vorländer,Matthias Kopano via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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<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:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span lang="EN-US" class="">Dear all,<span class="x_Apple-converted-space"> </span></span></div>
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<span lang="EN-US" class=""> </span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span lang="EN-US" class="">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></div>
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<span lang="EN-US" class=""> </span></div>
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<span lang="EN-US" class="">Thanks a lot in advance,</span></div>
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<span lang="EN-US" class="">Best,</span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span lang="EN-US" class="">Matthias</span></div>
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