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 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