1.  Getting the Data into CNS format

This is highly dependent upon how you processed the data.  If you processed it in mosflm, then your data will be in mtz format, which is what CCP4 uses.  It is a binary format, and CNS uses ascii formatted files.  There are various tools available to convert data within CNS, and there are also various tools in CCP4 that can help too.

For this example I will use the CCP4 program called mtz2various.  It is easiest to use this in the form of a shell script.


First, download the mtz files (these are the same as for the CCP4 example).


These include a hammerhead ribozyme native data set as well as two different Bromine derivative  data sets, which for obscure reasons I called derivative 123 and derivative  124.  There are no significant X-ray absorbering atoms in the native  data set, but Br absorbs X-rays quite significantly at the wavelength used  to collect these data sets (0.88 A if memory serves). Therefore both derivatives  contain useful anomalous differences as well.  Anomalous differences  reported in the native data set are essentially noise.

The data you just downloaded is in the form of a tarball, i.e., you have  to issue the commands:

% gunzip all_data.tar.gz  ; tar xvf all_data.tar.gz

or on some systems, simply

% tar xvfz all_data.tar.gz  

and you will get three files, each having the suffix mtz.  I called  the native data set  nomnph5.mtz and the two derivatives      124_trunc_anom.mtz       and    R_123_trunc_anom.mtz .  For this example we are only going to use the native and derivative 124, although you are welcome to use 123 as well.


Now we will use the CCP4 program mtz2various twice:


Make a file called mtz2cns.csh and put the following lines in it:

#!/bin/tcsh
mtz2various hklin 124_trunc_anom.mtz HKLOUT 124_CNS.hkl  <<eof
LABIN  FP=F124 SIGFP=SIGF124 DP=DANO124 SIGDP=SIGDANO124
OUTPUT CNS
END
eof

Make the shell script executable by issuing

% chmod +x mtz2cns.csh

Now run it.  Your output will look like this:


NREFlection=          11059
 ANOMalous=TRUE                                                                
 DECLare NAME=FOBS         DOMAin=RECIprocal   TYPE=COMP END                   
 DECLare NAME=SIGMA        DOMAin=RECIprocal   TYPE=REAL END                   
 INDE     0    0   12 FOBS=     865.0       0.0 SIGMA=     12.91               
 INDE     0    0   15 FOBS=     141.9       0.0 SIGMA=      5.44               
 INDE     0    0   18 FOBS=      28.2       0.0 SIGMA=     16.46               
 INDE     0    0   21 FOBS=      26.7       0.0 SIGMA=     16.43




Now edit the file and change FOBS to F124 and SIGMA to SIG124.  Here is my copy of the data file in case the above is problematic.  

Now change the shell script to reformat the native data.  Since this data does not have any anomalous scatterers, the shell script is simpler:

#!/bin/tcsh
mtz2various hklin nomnph5.mtz HKLOUT native.hkl  <<eof
LABIN  FP=Fnomnph5 SIGFP=SIGFnomnph5  
OUTPUT CNS
END
eof

You can leave it as FOBS and SIGMA this time.  Again, here is my copy, called native.hkl.