RCSB Map Generation
E-density map generation from RCSB-deposited model and structure factors
Related web sites:
Overview:
Using a set of RCSB-deposited coordinates and structure factors, the following
scripts can be used to generate a 2fo-fc electron density map surrounding
the model. Before using the scripts, copy the PDB (filename.pdb)
and structure factor (filename.ent) files to the following names:
pdb_file.pdb and sf_file.ent, respectively. Structure
factors from the RCSB are in mmCIF format. These typically can also
have the information from the header from the corresponding PDB file (lines
beginning with REMARK). The mmCIF header itself, within this overall
header, describes the nature of the actual structure factor columns; so
far two formats have been encountered. The first format (see short_sf_format.txt)
has 5 columns of data (h, k, l, F, sigF), and the second format (long_sf_format.txt)
has 8 columns (wavelength id, crystal id, h, k, l, F, sigF, FreeR flag).
In the scripts below the headers from the structure factor files are
first removed, and the long format file is reformated to a 5 column format.
In both cases, a 5 column ascii file with just structure factors results
(sf_file.fmt). This file is read by SFTOOLS to generate an
mtz file (sf_file.mtz), which is then scaled to a structure factor
file generated from the coordinates (sf-calc), giving rs-sfcalc.
The map is generated with fft from rs-sfcalc and the model-calculated
phases. The map is extended around the model with mapmask.
Finally, mapman is used to generate a normalized, brix format map file,
brixn_pdb_2fofc.map.
Intermediate files are deleted.
Several lines need to be edited in the following scripts (see headers
of the scripts) to add cell parameters, space group, and resolution for
the PDB file of interest.
Shell scripts to get to a map: