2 MAP_CALC Keyword: maps, calculate, MAP_CALC File: map_calc.txt Last modified: 8-oct-2010 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 CALC_MAP Keyword: calculate maps, map GUI, create_map_calc.pl 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 4 help prints this message with available options and current status 4 map map of [2FOFC+FOFC/2FOFC/FOFC/PHASE_COMB/FOBS/FCALC/3FO2FC] [2FOFC+FOFC] 5 2FOFC+FOFC Keyword: 2FOFC+FOFC, difference maps Calculates both types of difference maps. Does not work with kick maps. 5 2FO-FC Keyword: 2FO-FC_MAP, map, calculate, calc_fofc_diff_map.cmds 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: - integer map number of a unit cell map (MAP_2FOFC) - real number multiplier of Fobs = 2.0 - real number multiplier of Fcalc = 1.0 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 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: - integer map number of a unit cell map (MAP_FOFC) - real number multiplier of Fobs = 1.0 - real number multiplier of Fcalc = 1.0 5 PHAS_CMB Keyword: PHAS_CMB, phase combination, phase_comb.cmds, create_phase_comb.pl 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: - character variable or string of segment names used for structure factor calculations. - integer map number of a unit cell map (MAP_WORK) and 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). You can use your own files. 4 omit Calculates an "OMIT" map [ON/OFF]. When "ON" all key "active" atoms are excludedfrom structrue factor calculation. 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. See also "MAIN_DOC:refine/refine.txt". 4 target Keyword: ML map, UN map, maximum likelyhood, sigma A, map 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.txt". 4 generation Calculates [FIRST/SECOND/THIRD] generations of maps - omitting the MAP nonconsistent atoms for the subsequent structrue factor calculation. 4 way 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. 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 number Defines the MAP number [1/2/3/4/5/6/7/8/9/10] [1] in to which map will be loaded. 4 sharp Keyword: B-value sharpening B-factor sharpening for maps [ON/OFF] [OFF] 4 sharp_fact B-factor sharpening factor [30] 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 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 "generate_map.cmds" 3 KICK_0.3 Keyword: KICK_0.3, kick map 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. 3 KICK_?? Keyword: KICK_??, kick map, average of 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. 3 KICK_SEED Keyword: KICK_SEED, kick seed, kick 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 3 MAP_+_?? Keyword: MAP_+_?? 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. 3 KICK_MAP Keyword: KICK_MAP For orientation: - At 3.A resolution kicks up and even beyond 0.8A are meaningful. At last 6 different maps should be averaged. - At 2.0A resolution kick up to 0.3 are reasonable. At last 3 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. 3 OMIT_MAP Keyword: OMIT_MAP, omit map 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.