2 MAP_ATOM Keyword: maps, refinement, envelopes, skeletons File: map_atom.txt Last modified: 27-sept-2002 MAP_ATOM menu block covers transformations and interchange of information between atoms, maps (including envelopes) and structure factor data. It is loaded with the "MAIN_CMDS:load_map_atom.com" 3 RE_PHASE Keyword: R-value Calculates structure factors (PHASES) and R-factor of your current model. 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 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 writen to a file and read by MAIN, which then based on given FOBS, PHASES and WEIGHTS calculates a new FOBS map. You have to provide your own local shell script. MAIN calls R. Read program SIGMAA, a program from CCP4, for phase combination procedure. The "menu_phase_comb.sh" tool will create for you the necessary macors. 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 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 3FO-2FC_MAP Keyword: 3FO-2FC_MAP, map, calculate, calc_fofc_diff_map.cmds Calculates an 3Fobs-2Fcalc map from the last calculated structure factors using the "MAIN_CMDS:calc_fofc_diff_map.cmds" macro. Subroutine arguments: - integer map number of a unit cell map (MAP_2FOFC) - real number multiplier of Fobs = 3.0 - real number multiplier of Fcalc = 2.0 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. 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. 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 REF_DENS Keyword: REF_DENS, real space, density target Sets the target function for refinement ( variable "REF_METHOD" is set to "REF_DENS") to the density target, which will be used by the following "REFINE" click. Since the target map does not change during refinement also partial models can be fitted to experimental maps. Especially useful to improve NCS superposition parameters for density averaging procedures. 3 REF_DIFF Keyword: REF_DIFF, refinement, density, target, real space, difference density Sets the target function for refinement ( variable "REF_METHOD" is set to "REF_DIFF") to the difference density target, which will be used by the following "REFINE" click. The difference density map will be recalculated after a certain number of steps. Also derivateves are simplified to just a few density points. 3 REF_XLSQ Keyword: REF_XLSQ, refinement, least square target Sets the target function for refinement ( variable "REF_METHOD" is set to "REF_XLSQ") to the least square target, which will be used by the following "REFINE" click. This is the regular positional refinment target function. 3 KICK_ALL Keyword: KICK_ALL, kick atoms KICK_ALL displaces all "WORK_SEGM" atoms up to the current "KICK_VAL" shift. 3 REFINE Keyword: REFINE, refinement, positional, refine.cmds Refines positions of your model using macro "refine.cmds". Use main config tool "menu_refine.sh" to configure the macro. Subroutine arguments: - integer map number of a unit cell map (MAP_WORK) and - character variable or string(s) of segment names used for structure factor calculations. For more see "MAIN_DOC:refine/refine.txt". 3 REFINE_B Keyword: REFINE_B, b-factor, refinement, overall, individual, refine_b.cmds Refines B-values of a model (individual and overall) against the chosen target function using macro "refine_b.cmds". Refines positions of your model using macro "refine_b.cmds". Use main config tool "menu_refine_b.sh" to configure the macro. Subroutine arguments: - integer map number of a unit cell map (MAP_WORK) and - character variable or string(s) of segment names used for structure factor calculations. For more see "MAIN_DOC:refine/refine.txt". 3 GEN_SOLVENT Keyword: GEN_SOLVENT, solvent, generate Generates new solvent molecules on the basis of peaks in a difference density map, checks their consistency within an 2Fo-Fc map, their distance to hydrogen bond donnors and overlap with already existing atoms and symmetry overlap. The newly created solvent molecule (H2O) obtain segment name WAT2. HINT: Modify your RE_IMAGE command to see the newly created solvents in a different color. The macro invoked by default is the file "MAIN_CMDS:gen_solvent.cmds", which calls "MAIN_UTILS:gen_solvent.com", created by "menu_gen_solv.sh" script. Subroutine "gen_solvent.com" arguments: - integer map number of a 2fo-fc unit cell map (MAP_2FOFC), - integer map number of a fo-fc unit cell map (MAP_FOFC), - character variable or string(s) of segment names around which new solvents will be added, - character variable or string(s) of segment names around which new solvents will be added, which do not include any solvent molecule in order to enable control of solvent layers added. 3 WEI_AUTO Keyword: WEI_AUTO, weights, density Sets weights to atoms and residues by checking their positioning in a density map (MAP_2FOFC or MAP_FO). In combination with the ordinary RE_IMAGE gives you and idea where the model is reliable and where not. The default macro is "MAIN_CMDS:auto_stuff_weight.cmds" which calls the actual automatic weighting procedure "MAIN_UTILS:set_weight_auto_loop.com"