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gregdp / mapq

MapQ is a plugin for UCSF Chimera to calculate Q-scores of an atomic model in a cryoEM map.
https://cryoem.slac.stanford.edu/ncmi/resources/software/mapq
MIT License
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path_to_chimera needs to point to the binary for SBGrid installed Chimera on Mac OS #2

Closed rediaz111 closed 4 years ago

rediaz111 commented 4 years ago 
RED:[mapq_chimera] - python mapq_cmd.py /opt/sbgrid/i386-mac/chimera/1.14/ ~/Downloads/mapq_chimera/run_class001_1_2_3D_3.09.mrc ~/Downloads/mapq_chimera/6bdf_real_space_refined__Q__run_class001_1_2_3D_3.09.pdb
mapq_cmd.py
 -> this script
/opt/sbgrid/i386-mac/chimera/1.14/
/Users/rediazr/Downloads/mapq_chimera/run_class001_1_2_3D_3.09.mrc
 -> map or model
/Users/rediazr/Downloads/mapq_chimera/6bdf_real_space_refined__Q__run_class001_1_2_3D_3.09.pdb
 -> map or model

 - Please specify path to Chimera. If specified, the script may not have found a valid path.
RED:[mapq_chimera] - python mapq_cmd.py /opt/sbgrid/i386-mac/chimera/1.14/Chimera.app ~/Downloads/mapq_chimera/run_class001_1_2_3D_3.09.mrc ~/Downloads/mapq_chimera/6bdf_real_space_refined__Q__run_class001_1_2_3D_3.09.pdb
mapq_cmd.py
 -> this script
/opt/sbgrid/i386-mac/chimera/1.14/Chimera.app
 -> Chimera path, Mac
/Users/rediazr/Downloads/mapq_chimera/run_class001_1_2_3D_3.09.mrc
 -> map or model
/Users/rediazr/Downloads/mapq_chimera/6bdf_real_space_refined__Q__run_class001_1_2_3D_3.09.pdb
 -> map or model
gregdp commented 4 years ago

Thanks, interesting scenario, though I think it's ok because the Chimera.app is more like a folder rather than the binary itself. In think the binary in this case is Chimera.app/Contents/MacOS/chimera. Let me know if not and there are still issues running it, I could probably make it a bit smarter about finding the binary in the first case, or maybe even better, make the path to Chimera the path to the actual binary, which may avoid confusion (though then it requires a bit more digging on the part of the user).