2 MAP_CALC Keyword: maps, calculate, MAP_CALC File: map_calc.txt Last modified: 13-sept-2006 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". 3 BULK_SOL Keyword: BULK_SOL, bulk solvent, correction, partial structure factors Bulk solvent correction: toggles the flag ON or OFF. The actual optimization of linear and exponential coefficient is performed each time when "RE_PHASE" is clicked. See also "MAIN_DOC:calc_map/calc_map.txt" and "MAIN_DOC:refine/refine.txt". 3 ANISO_B 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 "RE_PHASE" is clicked. See also "MAIN_DOC:calc_map/calc_map.txt" and "MAIN_DOC:refine/refine.txt". 3 ML_MAP Keyword: ML_MAP, maximum likelyhood, sigma A Maximum likelyhood map: toggles the flag ON or OFF. When "ON" the "sigma A" formulation of maps is used during the actual map calculation (clicking on "FO-FC_MA" or "2FO-FC_MA". When of the least square weighting is used. It only works when the "TEST" reflection set has been defined. See also "MAIN_DOC:calc_map/calc_map.txt". 3 RE_PHASE Keyword: RE_PHASE, Fcalc, R-value, R-work, R-free Calculates structure factors (PHASES) and R-factors (R-work and R-free) of your current model. When the "TEST" set is not defined, the whole data set is used as the "WORK". The file "MAIN_CMDS:re_phase.cmds" is the default macro and it usually works fine. You can use your own files, by providing your local file. Subroutine arguments: - integer map number of a unit cell map (MAP_WORK) and - character variable or string of segment names used for structure factor calculations. 3 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 See also "MAIN_DOC:calc_map/calc_map.txt". 3 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. The file "MAIN_CMDS:calc_fo_map.cmds" is default file that you can tailor to your needs. Subroutine arguments: - integer map number of a unit cell map (MAP_FO) 3 2FO-FC_MAP 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 3 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 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.