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.
When using the right mouse button Tk GUI is invoked
create_map_calc.pl
-h|--help) prints this message with available options and current status
-m|--map) map of [2FOFC+FOFC/2FOFC/FOFC/PHASE_COMB/FOBS/FCALC/3FO2FC] [2FOFC+FOFC]
-o|--omit) omit map [ON/OFF] [OFF]
-b|--bulk) bulk solvent correction [ON/OFF/USE] [ON]
-a|--aniso) anisotropic overall correction [ON/OFF/USE] [ON]
-t|--target) target function [UN/ML] current = [ML]
-g|--generation) map generation [FIRST/SECOND/THIRD] current = [FIRST]
-y|--way) map ways [SINGLE/KICK] current = [SINGLE]
-k|--kick) maximal xyz kick size [0.0 - 1.33] current = [0.8]
-r|--random) kick size can be [FIXED/RANDOM/SERIES] = [FIXED]
-c|--steps) kick steps for averaging current = [30]
-n|--number) MAP number [1/2/3/4/5/6/7/8/9/10] [1]
-s|--sharp) B-factor sharpening for maps [ON/OFF] [OFF]
-f|--sharp_fact) B-factor sharpening factor [30]
-p|--precision) precision of density generation [1/2/3/4/5/6/7/8] [7]
-w|--write) write map files [ON/OFF] [OFF]
--doit) create the macro
prints this message with available options and current status
map of [2FOFC+FOFC/2FOFC/FOFC/PHASE_COMB/FOBS/FCALC/3FO2FC] [2FOFC+FOFC]
Calculates both types of difference maps. Does not work with kick maps.
Calculates an 2Fobs-Fcalc map from the last calculated structure factors using the MAIN_CMDS:calc_fofc_diff_map.cmds macro. It depends on the "ML_MAP" item. When on it used maximum likelyhood weighting and when off the least square weighting of resolution bins.
Subroutine arguments:
Calculates an Fobs-Fcalc map from the last calculated structure factors using the MAIN_CMDS:calc_fofc_diff_map.cmds macro. It depends on the "ML_MAP" item. When on it used maximum likelyhood weighting and when off the least square weighting of resolution bins.
Subroutine arguments:
MAIN calculates model structure factors via the "RE_PHASE" macro 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.
Subroutine arguments:
Calculates an Fobs map on the basis of the read Fobs, corresponding phases and weights (figure of merit). You can use your own files.
Calculates an "OMIT" map [ON/OFF]. When "ON" all key "active" atoms are excludedfrom structrue factor calculation.
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.
See also MAIN_DOC:refine/refine.html.
Maximum likelyhood maps [ML] or uniform weight [UN] maps are calculated.
"ML" uses the "sigma A" formulation of maps weighting, whereas for "UN" the least square weighting is used. "ML" only works when the "TEST" reflection set has been defined.
See also MAIN_DOC:calc_map/calc_map.html.
Calculates [FIRST/SECOND/THIRD] generations of maps - omitting the MAP nonconsistent atoms for the subsequent structrue factor calculation.
Map can be caluclated by two different ways [SINGLE/KICK]. "SINGLE" implies that the current set of atoms is being used, whereas for "KICK" maps a series of randomly displaced positions are being used.
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]
Defines the MAP number [1/2/3/4/5/6/7/8/9/10] [1] in to which map will be loaded.
B-factor sharpening for maps [ON/OFF] [OFF]
B-factor sharpening factor [30]
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.
During map calculation each map generation can be stroed to a file for later use. write map files [ON/OFF] [OFF]
Create the macro "generate_map.cmds"
Choose the displacement parameter ("KICK_0.3" or KICK_??"). For refinement 0.3 is maximum tolerated by the minimizer, whereas for kicked map much larger kicks (see"KICK_??") can be specified") can be specified.
Choose the displacement parameter ("KICK_0.3" or KICK_??"). For refinement 0.3 is maximum tolerated by the minimizer, whereas for kicked map much larger kicks can be specified"kicked map much larger kicks can be specified.
Sets the strating "SEED" for the random number generator. At each call, the seed variable "RAN_SEED" is increased for 1. The "RAN_SEED" is "MAIN" internal variable, which value can be directly set and inspected using the MAIN syntax:
> set vari RAN_SEED > show vari RAN_SEED
The number of maps generated by a different random number seed to average ("MAP_+_??"). The rule of a thumb is at least the kick parameter*10 repetitions.
For orientation:
last 6 different maps should be averaged.
With zero kick and averaging of 1 maps the resulting map is pure 2Fo-Fc map.
Averaged "2FO-FC" map is calculated by clicking "KICK_MAP".
Note that averaging "ML_MAP" maps occasionaly result in maps worse that the "ML_MAP" without kicking.
An averaged omit map is calculated by clicking "OMIT_MAP". With zero kick and averaging of one maps the resulting map is pure Fo-Fc map. The parts selected in the current key "active" are omitted from structure factor calculation. Apply the same kicks and numbers of maps for averaging as for the kick maps.