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
<read.com <map_io.cmds <refine_all.cmds
write over file SAVE_FILE_refined.pdb atom pdb
EOF
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 EOF
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 <read.com 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
quit EOF
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 return
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 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
No MTZ file - SHELX and SCALEPACK
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
or
create_read.pl -s p21_21_21 --diffr my.sca --diffr_form SCALEPACK --doit