2 MAP_DO Keyword: maps, calculate, MAP_CALC, MAP_IO File: map_do.txt Last modified: 13-apr-2019 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.txt". 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. 3 MAP_IO Keyword: read map, write map, mrc, format, MAP_IO 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 4 doit Create the macro "map_io.cmds" 3 CALC_MAP Keyword: calculate maps, map GUI, create_map_calc.pl 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 4 help prints this message with available options and current status 4 atoms atoms by [ALL/WORK_SEGM/SEGMENTS/SELECTION] [WORK_SEGM] Specifis how selection of atoms for structure factor calculation and later map is created. 4 map Keyword: map, calculate, calc_fofc_diff_map.cmds map of [2FOFC+FOFC/2FOFC/FOFC/PHASE_COMB/FOBS/FCALC/3FO2FC/REFINE] [2FOFC+FOFC] Specifies which kind of map will be calculated. 5 2FOFC+FOFC Keyword: 2FOFC+FOFC, difference maps Calculates both types of difference maps. Combination does not work with kick maps. 5 2FO-FC Keyword: 2FO-FC_MAP, Calculates an 2Fobs-Fcalc map from the last calculated structure factors. 5 FO-FC_MAP Keyword: FO-FC_MAP, map, calculate, calc_fofc_diff_map.cmds Calculates an Fobs-Fcalc map from the last calculated structure factors. 5 PHAS_CMB Keyword: PHAS_CMB, phase combination, phase_comb.cmds, create_phase_comb.pl 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. 5 FOBS_MAP Keyword: FOBS_MAP, map, calculate, calc_fo_map.cmds Calculates an Fobs map on the basis of the read Fobs, corresponding phases and weights (figure of merit). 5 FCALC Calculates an Fcalc (Fmodel) map. 5 3FO2FC Calculates an 3Fobs-2Fcalc map. 5 REFINE Calculates maps use din real space refinement. 4 number 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. 4 target target function [FREE_KICK/CROS_CORR/UN/SIGMA/PATTERSON] current = [FREE_KICK] 5 FREE_KICK Calculates a free kick maximum likelihood map. It does not depend on the TEST set of reflections. It is the default map. 5 CROS_CORR Calculates a cross correlation maximum likelihood map. It depends on the TEST set of reflections. 5 UN Calculates an unweighted map. 5 SIGMA Calculates an sigma weighted map. 5 PATTERSON Not finished. 4 bulk Keyword: BULK_SOL, bulk solvent, correction, partial structure factors 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.txt". 4 aniso Keyword: ANISO_B, anisotropic, overall, correction 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. 4 omit Calculates an "OMIT" map [ON/OFF]. When "ON" all key "active" atoms are excluded from the structure factor calculation. 4 generation 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. 4 way 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. 4 kick Maximal xyz kick size [0.0 - 1.33] current = [0.8] 4 series Kick size can be [FIXED/RANDOM/SERIES] = [FIXED] 4 steps Specifies the number of steps for KICK map averaging. default = [30] 4 missing Include Fmodel structure factors for missing Fobs [YES/NO] [YES] 4 sharp Keyword: B-value sharpening B-factor sharpening for maps [ON/OFF] [OFF] 4 sharp_fact B-factor sharpening factor [30] 4 density -d|--density) grid density per resolution [3] 4 zones -z|--zones) number of zones - 0 for auto [0] 4 scale 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. 4 crystal crystal for maps [1/2/BOTH] current [1] Calculates density maps for crystal form 1, 2 or BOTH. 4 Rfree R-free flag [ON/OFF] current [OFF] 4 precision 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. 4 badd b-factor add value for FFT - 0 for auto [0] 4 write During map calculation each map generation can be stroed to a file for later use. write map files [ON/OFF] [OFF] 4 doit Create the macro "map_calculate.cmds"