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.
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.html and 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 "RE_PHASE" is clicked.
See also MAIN_DOC:calc_map/calc_map.html and MAIN_DOC:refine/refine.html.
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.html.
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:
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:
See also MAIN_DOC:calc_map/calc_map.html.
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:
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:
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.