High throughput setup

Read molecule, map and minimize

Prepare minamal working environment for MAIN. Create the "read.com":

 create_read.pl --atom SAVE_FILE.PDB -doit

Read unit cell size xmap into the target map "3" via creation of "map_io.com":

 create_map_io.pl  --task READ --file my_map.xmap --target 3 --doit

Create the real space refinement macro against map "3" with

 create_refine_all.pl --target MAP --map 3 --xyz 30 --overall -1 --bfactor -1 --occupancy -1 --doit

Create the macro for running the procedure:

Run the procedure:

mainps --nodisplay<< EOF


 write over file SAVE_FILE_refined.pdb atom pdb


To add cyclic kicking

 create_refine_all.pl --target MAP --map 3 --xyz 30

Generate density map from atoms

create unit cell "cell.dat" file

cat<< EOF
 100 100 100 90 90 90

Use the "read.com" above to read a PDB file. Then create map and fill it with atomic density of atoms with B-value of 30 and write the output map.

mainps --nodisplay<<EOF
 set temp sele all end = 30
 set vari THE_MAP = 1

 make map THE_MAP grid 100 100 100 box 0 0 0 99 99 99 ZERO init 0 real

 make map THE_MAP -
           atom dens -
           sele all end

 write over file my_density.xmap map THE_MAP xplor


A complex: macromolecule with an inhibitor

 create_main_config.pl -u my.mtz -m A INH --doit
 create_read.pl -i MODEL -t get_my_top_par.com --doit
 cp my_vers_0.pdb my_inh.pdb SAVE_FILE.PDB

Where "my.mtz" is the diffraction data file, "A" and "INH" are segment IDs of a macromolecule and inhibitor and "get_my_top_par.com" is a macro script written in MAIN language reading additional topology and parameter files for hetero compounds in xplor (CNS) format:

 read file my_ing.top top xplor
 read file my_inh.par par

The "my_vers_0.pdb" is the "PDB" input of atomic coordinates file and "my_inh.pdb" is teh inhibitor file. They are copied to the "SAVE_FILE.PDB", which is the default name for the coordinates input. It is recommended to keep the name and save temporary copies under some other.

MTZ does not convert properly

MTZ is a binary file and it happes that due to the differences in computer architecture the form of floating point may not be properly understood by "use_mtz.pl". In this case the native conversion must be switched off (mtz2various will be invoked in the background):

 use_mtz.pl --mtz my.mtz --native OFF --doit


The "create" scripts extract unit cell and cell constants only from an "mtz" file (alternatively these data may be extracted from the PDB file), otherwise the cell constants file has to be created. The default name is "cell.dat". It contains 6 numbers in free format.

  89. 167. 89. 90. 120. 90.

The space group has to be provided to the "create_read.pl" script as well as the file name and format of the reflection data file:

 create_read.pl -s p21_21_21 --diffr my_shelx.hkl --diffr_form SHELX --doit


 create_read.pl -s p21_21_21 --diffr my.sca --diffr_form SCALEPACK --doit