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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 map and check consistency with the experimental data:
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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 [```prepare_locscale_input.py```](prepare_locscale_input.py) script.
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In the following the procedure is illustrated for TRPV1 channel [1]. The files can be found [here](http://emsearch.rutgers.edu/atlas/5778_downloads.html)
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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 map and check consistency with the experimental data using the provided [```prepare_locscale_input.py```](prepare_locscale_input.py) script.
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<br>
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In the following the procedure is illustrated for TRPV1 channel [1] from the EMDB Model Challenge [2]. All required files can be found [here](http://emsearch.rutgers.edu/atlas/5778_downloads.html).
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```
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phenix.python prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778_full.map
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```
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###### This procedure generates three files:
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##### This procedure generates three files:
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- `pdb3j5p_4locscale.pdb` (shifted) PDB model with same P1 unit cell as map
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- pdb3j5p_4locscale.pdb (shifted) PDB model with same P1 unit cell as map
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- `pdb3j5p_4locscale.mrc` Reference model map
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- `emd_5778_full_4locscale.mrc` (shifted) original reconstruction
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<br>
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By default structure factors from the model are computed to Nyquist frequency. This is the preferred procedure for LocScale processing.
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A different resolution cut-off can be supplied using the ```-dmin``` flag. See
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```
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phenix.python prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778_full.map -dmin 4.0
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```
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See [```prepare_locscale_input.py```](prepare_locscale_input.py) script for further options.
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#### Link to [source](https://git.embl.de/jakobi/LocScale/blob/master/prepare_locscale_input.py)
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[recommended procedure](model_map_generation_from_arbitrary_files)
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#### __PLEASE download the following [electron form factor table](electron_scattering.py) for use with pdb2map.py.__
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[[1]](https://www.nature.com/nature/journal/v504/n7478/full/nature12822.html) Liao et al., _Nature_ __504__:107-112 (2013) |
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[[1]](https://www.nature.com/nature/journal/v504/n7478/full/nature12822.html) Liao et al., _Nature_ __504__:107-112 (2013)
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[[2]](http://challenges.emdatabank.org/?q=model_challenge) EMDB Model Challenge 2015/2016 |
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