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#### Model map generation from a PDB coordinate model
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To produce the desired result of locally contrast-optimized maps, LocScale requires a reference model map that accurately reflects the variation in resolution and contrast expressed in atomic B-factors. We therefore highly recommend to first perform coordinate refinement against a globally sharpened and locally filtered map as described in our BioRxiv preprint.
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The model map can be generated by any procedure that computes the model map from B-factor weighted structure factors using electron scattering atomic form factors. We here provide a recommended procedure to generate the model maps:
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__Note that normally steps 1-3 are not required if model and map have already been refined__
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<br>
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__(1)__ The EM map should be zero-based, i.e. the map origin should be located at (0,0,0). The [```check_and_set_ori_zero.py```](check_and_set_ori_zero) script is a quick way to ascertain the map is zero-based.
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__(2)__ If the map was already zero-based this step can be skipped. If the map was shifted in (1), the PDB model should be shifted by the same amount in real coordinates (i.e. voxel_shift*pixel_size).
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- Open model and map in Chimera (```chimera em_map.mrc pdb_model.pdb &```)
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- Shift model to fit with zero-based map (```move -45 -45 -45 model #1 coord #1```)
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- Save model relative to map coordinates (```write format pdb relative #1 #0 filename.pdb```)
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__(3)__ Check if PDB symmetry matches that of EM map.
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To generate a model map with B-facvtor weighted structure factors and electron form factors we recommend to use the provided [```pdb2map.py```](pdb2map.pyc) script.
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```
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usage: prepare_locscale_input -mc model.pdb -em map.ccp4 [-dmin resolution] [-h]
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[--out OUT] [--table TABLE] [--apix APIX] [--radius RADIUS]
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[--bfactor BFACTOR] [--verbose]
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*** Computes reference map from PDB model and generates files for LocScale ***
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Input:
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-mc model.pdb, --model model.pdb
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Input filename PDB
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-em map.ccp4, --map map.ccp4
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Input filename map
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Options:
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-dmin resolution map resolution
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-h, --help show this help message and exit
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--out OUT Output filename RSCC table
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--table TABLE Scattering table [electron, itcc]
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--apix APIX pixel size [A]
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--radius RADIUS atom radius [A]
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--bfactor BFACTOR set bfactor [A^2]
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--verbose print result to stdout
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```
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#### __PLEASE download the following [electron form factor table](electron_scattering.py) for use with pdb2map.py.__ |
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\ No newline at end of file |