All files for this example are on hermione in directory:
       /home/dave/ccp4_examples/L9_n27c_MR/

In this case, the molecular replacement is done using MOLREP (a program
within CCP4), and refined using anneal.inp in CNS.

The structure of L9 mutant N27C has 2 molecules in the asymmetric unit.  This is
different from L9 wild-type, which has one molecule in the asymmetric unit,
crystallized in a different space group.

The unit cell dimensions of L9 N27C are:

a = 131.7
b = 37.5
c = 101.7
space group = P212121

(compare this with wild-type L9, which is a much smaller unit cell of
   a = 135.3, b= 37.3, c = 49.0)

To get started, two things are needed:

    1) A search model for the structure. In this case, L9_mr_model.pdb is used.
       This model contains about 2/3 of the L9 wild-type structure.

    2) X-ray data for mutant L9 N27C.  This is called "L9_n27c.mtz", and is in
       CCP4 format. The data goes to about 2.9 A resolution.
 

Step 1: Do Molecular replacement using MOLREP.
        The script for this is a file called "molrep_n27c.sh" :

#!/bin/sh
molrep HKLIN L9_n27c.mtz \
       MODEL L9_mr_model.pdb<<stop
DOC  Y
LABIN F=Fnat  SIGF=Snat
#NP    10      - number of peaks of rotation function to be checked.
#                   Maximum: 50. Default: 10
#NPT   20      - number of peaks of translation function to be checked.
#                   Maximum: 50. Default: 20
#NMON   1      - number of monomers. Program will try to create full model
NMON   2
NP     3
NPT    10
END
stop
#
 

The output from molrep is a PDB file with the chains of both molecules that
are in the asymmetric unit. It is called "molrep.pdb".
 

Step 2: Refine the L9 N27C structure using CNS:

First must convert x-ray data to CNS format, using "mtz2cns.sh" script:

#!/bin/csh -f
mtz2various \
hklin L9_n27c.mtz \
hklout n27c.cns  \
<<eof
OUTPUT CNS
labin FP=Fnat SIGFP=Snat
END
eof
#
 
 

Next, must add free-R flag to data, using "make_cv.inp".

Next, must generate ".mtf" file and CNS-format PDB file using "gen_dimer.inp".

Next, do annealing to refine structure using "anneal.inp".

Finally, calcuate map using "model_map.inp".

        Here is a view of the map, as a JPEG file.

All files for this example are on hermione in directory:

       /home/dave/ccp4_examples/L9_n27c_MR/