... | @@ -10,13 +10,14 @@ In the following the procedure is illustrated for TRPV1 channel [1] from the EMD |
... | @@ -10,13 +10,14 @@ In the following the procedure is illustrated for TRPV1 channel [1] from the EMD |
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phenix.python prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778_full.map
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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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```
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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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- `pdb3j5p_4locscale.mrc` __Reference model map__
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- `emd_5778_full_4locscale.mrc` (shifted) original reconstruction
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- `emd_5778_full_4locscale.mrc` __(shifted) original reconstruction__
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<br>
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<br>
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The two MRC maps are to be used for input in the LocScale procedure.
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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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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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A different resolution cut-off can be supplied using the ```-dmin``` flag. See
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... | @@ -32,6 +33,6 @@ LocScale maps can be computed using any source of reference maps for scaling. If |
... | @@ -32,6 +33,6 @@ LocScale maps can be computed using any source of reference maps for scaling. If |
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[//]: # (#### __PLEASE download the following [electron form factor table](electron_scattering.py) for use with pdb2map.py.__)
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[//]: # (#### __PLEASE download the following [electron form factor table](electron_scattering.py) for use with pdb2map.py.__)
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References:
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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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[[2]](http://challenges.emdatabank.org/?q=model_challenge) EMDB Model Challenge 2015/2016 |
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\ No newline at end of file |