Experimental Map Generation

CCP4 map generation

See the website:

fft to generate fourier synthesis e-density map from h,k,l,phi file:

#!/bin/csh -f
#
/keck/CCP4_V33/bin/fft hklin solve3.mtz MAPOUT ccp4_solve3.map << eof
TITLE Map from 3 lambda from solve.mtz
reso 20.0 2.0
LABIN F1=FP PHI=PHIB W=FOM
END
eof
Solve3.mtz was the solvent-flattened output from SOLVE with MAD-derived phase estimates.

mapmask to extend the map:

#!/bin/csh -f
#
/keck/CCP4_V33/bin/mapmask mapin ccp4_fft.map mapout ccp4_mmsk7.map << eof
XYZLIM 10 120 10 120 55 205
END
eof


Here, x limits are 10 to 120, y limits are 10 to 120, and z limits are 55 to 205.  These ranges can be adjusted until e-density covers entire molecule.
 

Skeletonizing electron density

See the website:

For Uppsula Software Factory documentation including Mapman.

Mapman:

mapman
MAPMAN> re m1 ccp4_mmsk7.map ccp4
MAPMAN> no m1
MAPMAN> br m1 brixn_mmsk7.map
MAPMAN> bo sk m1 1.5 0.5 100
MAPMAN> bo co sk7.bones sk7
Min length main-chain fragments ? (           5)<CR>
Read in map file ccp4_mmsk7.map with buffer identifier "m1"; it is in ccp4 format (other options:  cns, xplor, brix).  Normalize (no) the map.  Output a new copy of the normalized map in brix format (br).  Generate the bones (bo sk) and then connect and write out the bones file (bo co).  The "sk7" identifier will appear in the header of the sk7.bones file; this will define the name of the datablock when reading into "O".