Electron density to VRML notes

gistfile1.txt

# Tools:
# sf-convert: http://sw-tools.pdb.org/apps/SF-CONVERT/doc/V1-0-00/documentation.html
# Coot
# CCP4
# Pymol

# Get mmCIF format structure factors, and PDB coordinates
wget http://www.rcsb.org/pdb/files/r4J1Ysf.ent.gz
wget http://www.rcsb.org/pdb/files/4J1Y.pdb.gz
gunzip r4J1Ysf.ent.gz 4J1Y.pdb.gz
mv r4J1Ysf.ent 4j1y-sf.cif

# Convert mmCIF to MTZ
~/programs/sf-convert-v1.204-prod-src/bin/sf_convert -o MTZ -sf 4j1y-sf.cif

# Load 4j1y-sf.cif.mtz in Coot, export a .map (ccp4 map format)
# TODO: Headless command or phenix/ccp4 equivalent without Coot

# In Pymol, set up a decent starting view
show ribbon, 4J1Y
hide lines, 4J1Y
save 4J1Y_ribbons.wrl, 4J1Y

# In Pymol, with the structure loaded, load the map and define an isomesh surface
load 4J1Y_FP.map, format=ccp4
isomesh map, 4J1Y_FP.map, 2.0, 4J1Y, carve=1.6
show mesh, map
color marine, map

# Make an isosurface and 'isodot' views
isosurface surf, 4J1Y_FP.map, 2.0, 4J1Y, carve=1.6
isodot dot, 4J1Y_FP.map, 2.0, 4J1Y, carve=1.6

# Mesh outputs as cylinders and spheres
save 4J1Y_isomesh.wrl, map
# Dots output as VRML spheres 
save 4J1Y_isodot.wrl, dot