MAP_CALC menu block includes items performing map calculations.
It is loaded with the MAIN_CMDS:load_map_calc.com
For more information see also MAIN_DOC:calc_map/calc_map.html.
The only reason for leaving the items appart from the "CALC"MAP"is that the "create_map_calc.pl"accessible via Tk GUI does not cover the mluticrystal map calculations"calculations.
create_map_io.pl
-h|--help) prints this message with available options and their current status
-x|--task) task to do [COPY/READ/SAVE_AS/MASK_IN/MASK_OUT] [COPY]
-s|--source) source MAP number [1/2/3/4/5/6/7/8/9/10] [2]
-t|--target) target MAP number [1/2/3/4/5/6/7/8/9/10] [3]
-y|--crystal) crystal target [1/2] [1]
-g|--grid) grid of the target map [0]
-r|--radius) mask atom radious [3]
-c|--contour) contour the target map at [1]
-b|--box) box of the target map [25]
-a|--color) color of the target map [RED/ORANGE/YELLOW/GREEN/CYAN/BLUE/WHITE] [CYAN]
-l|--label) map label [IO_MAP]
-p|--sharp) B-factor sharpening for maps [ON/OFF] [ON]
-t|--sharp_fact) B-factor sharpening factor: - desharp + sharp [0]
-s|--selection) mask in selection [active]
-f|--file) file name [my_map.xmap]
--doit) create the macro
Create the macro "map_io.cmds"
When using the right mouse button Tk GUI is invoked
create_map_calculate.pl -h|--help) prints this message with available options and current status -i|--atoms) atoms by [ALL/WORK_SEGM/SEGMENTS/SELECTION] [WORK_SEGM] -u|--selection) selection of atoms [segm name WORK_SEGM] -m|--map) map of [2FOFC+FOFC/2FOFC/FOFC/PHASE_COMB/FOBS/FCALC/3FO2FC/REFINE] [2FOFC] -n|--number) MAP number [1/2/3/4/5/6/7/8/9/10] [1] -t|--target) target function [FREE_KICK/CROS_CORR/UN/SIGMA/PATTERSON] current = [FREE_KICK] -b|--bulk) bulk solvent correction [ON/OFF/USE] [ON] -a|--aniso) anisotropic overall correction [ON/OFF/USE] [ON]
-o|--omit) omit map [ON/OFF] [ON] -g|--generation) map generation [FIRST/SECOND/THIRD] current = [FIRST]
-y|--way) map ways [NO_KICK/KICK] current = [NO_KICK] -k|--kick) maximal xyz kick size [0.0 - 1.33] current = [0.8] -r|--series) kick size can be [FIXED/RANDOM/SERIES/X_ERROR] = [FIXED] -v|--average) kick steps for averaging current = [30] -c|--missing_fc) include missing reflections [YES/NO] [YES]
-s|--sharp) B-factor sharpening for maps [ON/OFF] [OFF] -f|--sharp_fact) B-factor sharpening factor: - desharp + sharp [30]
-d|--density) grid density per resolution [3] -w|--write) write map files [ON/OFF] [OFF] -z|--zones) number of zones - 0 for auto [0] -l|--scale) r-value scale [AVERAGE/VARIOUS] [VARIOUS] -x|--crystal) crystal for maps [1/2/BOTH] current [1] -e|--free) r-free flag [ON/OFF] current [OFF] -p|--precision) precision of density generation [1/2/3/4/5/6/7/8] [7]
-+|--badd) b-factor add value for FFT - 0 for auto [0]
--doit) create the macro
prints this message with available options and current status
atoms by [ALL/WORK_SEGM/SEGMENTS/SELECTION] [WORK_SEGM]
Specifis how selection of atoms for structure factor calculation and later map is created.
map of [2FOFC+FOFC/2FOFC/FOFC/PHASE_COMB/FOBS/FCALC/3FO2FC/REFINE] [2FOFC+FOFC]
Specifies which kind of map will be calculated.
Calculates both types of difference maps. Combination does not work with kick maps.
Calculates an 2Fobs-Fcalc map from the last calculated structure factors.
Calculates an Fobs-Fcalc map from the last calculated structure factors.
MAIN calculates model structure factors and writes them to a file, which is processed by a phase combination program invoked via a shell command. The resulting phases are then written to a file and read by MAIN, which then based on given FOBS, PHASES and WEIGHTS calculates a new FOBS map.
MAIN calls R. Read program SIGMA A, a program from CCP4, for phase combination procedure. The "create_phase_comb.pl" tool will create for you the necessary macros.
Calculates an Fobs map on the basis of the read Fobs, corresponding phases and weights (figure of merit).
Calculates an Fcalc (Fmodel) map.
Calculates an 3Fobs-2Fcalc map.
Calculates maps use din real space refinement.
MAP number [1/2/3/4/5/6/7/8/9/10] [1]
Specifies the map number in which results of map calculation will apear.
target function [FREE_KICK/CROS_CORR/UN/SIGMA/PATTERSON] current = [FREE_KICK]
Calculates a free kick maximum likelihood map. It does not depend on the TEST set of reflections. It is the default map.
Calculates a cross correlation maximum likelihood map. It depends on the TEST set of reflections.
Calculates an unweighted map.
Calculates an sigma weighted map.
Not finished.
Bulk solvent correction is "ON/OFF/USE" [ON]
Bulk solvent correction: toggles the flag ON or OFF. The actual optimization of linear and exponential coefficient is performed each time when structure factor calculation is performed.
See also MAIN_DOC:refine/refine.html.
Overall anisotropic correction: toggles the flag ON or OFF. The actual optimization of the 6 parameters defining the anisotropic distorsion is performed each time when structure factors are calculated.
Calculates an "OMIT" map [ON/OFF]. When "ON" all key "active" atoms are excluded from the structure factor calculation.
map generation [FIRST/SECOND/THIRD] current = [FIRST]
Calculates [FIRST/SECOND/THIRD] generations of maps - omitting the MAP nonconsistent atoms for the subsequent structrue factor calculation.
map ways [NO_KICK/KICK] current = [NO_KICK]
Map can be calculated by two different ways [NO_KICK/KICK]. "NO_KICK" implies that the current set of atoms is being used, whereas for "KICK" maps a series of randomly displaced positions are being used. It is the averaged kick map.
Maximal xyz kick size [0.0 - 1.33] current = [0.8]
Kick size can be [FIXED/RANDOM/SERIES] = [FIXED]
Specifies the number of steps for KICK map averaging. default = [30]
Include Fmodel structure factors for missing Fobs [YES/NO] [YES]
B-factor sharpening for maps [ON/OFF] [OFF]
B-factor sharpening factor [30]
-d|--density) grid density per resolution [3]
-z|--zones) number of zones - 0 for auto [0]
r-value scale procedure [AVERAGE/VARIOUS] [VARIOUS]
"AVERAGE" calculates an average K and reciprocal space B-factor, whereas "VARIOUS" uses independet K for each zone and does not use overall B factor in scaling.
crystal for maps [1/2/BOTH] current [1]
Calculates density maps for crystal form 1, 2 or BOTH.
R-free flag [ON/OFF] current [OFF]
Precision of density generation [1/2/3/4/5/6/7/8] [7]. The lower numbers may speed up calculations on the cost of accuarcy.
b-factor add value for FFT - 0 for auto [0]
During map calculation each map generation can be stroed to a file for later use. write map files [ON/OFF] [OFF]
Create the macro "map_calculate.cmds"