There are no restrictions to where $file is in the script. But $file is only substituted if the open command forEachFile option is used.

Tom

On Aug 18, 2021, at 11:19 AM, Vorländer,Matthias Kopano matthias.vorlaender@imp.ac.at wrote:

Hi Tom,

Thanks a lot, this works 😊 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?

Thanks again for the amazing support, Best, Matthias

From: Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> Date: Wednesday, 18. August 2021 at 18:51 To: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at mailto:matthias.vorlaender@imp.ac.at> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Automated Fitting of models into maps and saving fits with a correlation score > X

Hi Matthias,

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

fitsearch #2 in #1 resolution 20 search 1000 cutoff 0.9 save Tomo_fitted_$file_%d.pdb

This is described in the forEachFile documentation

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile

Tom

On Aug 18, 2021, at 7:57 AM, Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at mailto:matthias.vorlaender@imp.ac.at> wrote:

Dear Tom,

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:

Open ChimeraX_Daily in no-gui mode Type “open FitPDBinVolume.cxc foreach *.mrc” The script FitPDBinVolume.cxc is very simple and looks like this:

open 7apk open /Volumes/matthias.vorlaender/Scripts/Chimera/fit_search.py 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

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?

Thanks a lot in advance, Best, Matthias

From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu mailto:chimerax-users-bounces@cgl.ucsf.edu> on behalf of "Vorländer,Matthias Kopano via ChimeraX-users" <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Reply to: "Vorländer,Matthias Kopano" <matthias.vorlaender@imp.ac.at mailto:matthias.vorlaender@imp.ac.at> Date: Tuesday, 27. July 2021 at 07:40 To: Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> Cc: "chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Automated Fitting of models into maps and saving fits with a correlation score > X

Hi Tom,

Thanks so much, that's amazing!

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.

Thanks a lot for your help, Best, Matthias

Holen Sie sich Outlook für Android https://aka.ms/AAb9ysg

From: Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> Sent: Tuesday, July 27, 2021 12:15:13 AM To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at mailto:matthias.vorlaender@imp.ac.at> Cc: chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Automated Fitting of models into maps and saving fits with a correlation score > X

Hi Matthias,

You can run ChimeraX command scripts or Python scripts without a GUI, just start it at the shell with the "--nogui" option, for example

chimerax --nogui mycommands.cxc

I made some example Python code that runs fitmap search and saves PDB files for each unique fit with correlation over 0.9.

https://rbvi.github.io/chimerax-recipes/fit_search/fit_search.html https://rbvi.github.io/chimerax-recipes/fit_search/fit_search.html

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.

Tom

Example search of monomers in 14-mer GroEL.

On Jul 25, 2021, at 9:05 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:

Dear all,

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?).

Thanks a lot in advance, Best, Matthias _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users