Scripts for non-crystallographic and multi-crystal averaging

 

Description:

This C-shell script called mc_ave.com is to do multi-crystal form averaging automatically with some auxiliary programs and an input file including experiment data. Its main program for multi-crystal averaging is MAVE from USF RAVE package, whose script is auto-generated by a jiffy program called CRAVE (also from USF RAVE package). If you haven¡¯t used MAVE before, please visit http://xray.bmc.uu.se/usf/ to learn more notes.  When using this C-shell script, you need not to generate NCS-operators, edit CRAVE script and convert density maps from mtz format to map format by yourself.

 

Copyright:

     Prof. Fei Sun¡¯s group, Institute of Biophysics, CAS, wrote these scripts.

    

Scripts files:

Follows are some requisite programs and files used in this C-shell script, which can be downloaded from here if you do not have any one of them.

mc_ave.com : main C-shell script.

crave_head.txt : a part of CRAVE script.

mask_gener.com : a program to generate mask file (O/MAMA format) written by Kai Zhang.

omap2ccp4.com : a program to convert density map from O/MAMA format to map format written by Kai Zhang.

ncs_op_gener : a program to generate NCS-operators written by Kai Zhang.

the PDB file which will be used in the process of generating mask (please prepare by yourself)

symmetry operators: "O" data block file which contains the symmetry operators for the spacegroup of the crystals, such as p212121.sym.

information.txt: a file including experiment data should be edited by users according to following rules. You can download an example from here for easier editing.

 

Usage:

Editing the files ¡°information.txt¡± for gathering important parameters:

1st row: absolute path where your CCP4 are installed (you can type ¡°echo $CBIN¡± to obtain)

2nd row: project name (you should give this project a name you like)

3rd row: absolute path where your experiment data including density maps (mtz format) and coordinate files (pdb files) are held

4th row: current work directory (absolute path)

5th row: number of crystals

6th row: the PDB file which will be used in the process of generating mask

7th row: cycles of multi-crystal form averaging

8th row: enter the information of crystals from this row on. The information of one crystal is written in one row. There are 5 columns in these rows, which are separated by TAB.

     1st column: name of the density map

     2nd column: name of the coordinate file

     3rd column: space group of the crystal represented by number, such as 19.

     4th column: space group of the crystal represented by short symbol , such as p212121.

     5th column: number of chains in the coordinate file

     Running the script:

     ./mc_ave.com    

 

Notes:

1.   The input density maps must be of mtz format.

2.   The labels of input density maps must be F=F, SIGF=SIGF. If your maps don not meet the demand, please use cad from CCP4 to merge your mtz files.

3.   The mask map will be generated in the first map you enter in information.txt according to the PDB file you provide.

4.   You¡¯d better make a new directory to run this script and make sure the data that has nothing to do with this project does not exit.

 

Output files:

final.omap: final averaged map with O/MAMA format

final.map: final averaged map with CCP4 format

mask.mask: mask map with O/MAMA format

mask.msk: mask map with CCP4 format

*.o: NCS-operators (extension name is ¡°o¡±)

¡°log¡± directory: directory holding all log files