Last modified: 14-feb-98
MINIMIZES a potential ENERGY function of the SELECTED ATOMS for a specified number of steps and writes the results. All ENERGY terms turned on are applied in the procedure. POSITIONS, B-VALUES and TRANSLATIONAL and ROTATIONAL parameters of a single rigid body can be optimized.
Before a POSITIONAL or B-VALUE minimization starts, the current data are saved internaly. See also MAIN_COM:energy.html and "UN_DO menu item MAIN_MENU:xray_build.html.
> show energy > energy > save coor restore
MINIMIZE STEP inte WRITE_STEP inte IMAGE_STEP inte BY CONJUGATED BODY SELECT ... END (SELECT ... END) KEY [select active end select passive end] LIST_GENERATION ON OFF TRANSLATE 3*(real inte) POLAR 3*(real inte) XYX-AXES 3*(real inte) GAIN_R-VALUE real POSITION B-VALUES OVERALL INDIVIDUAL PHASE ( STEPS inte MACRO file_name SELECT ... END FREE SELECT ... END KICK ( = real SEED inte LINEAR SQUARE EXPONENTIAL ) ) BASE = real KICK real (not working yet) RESCALE ON OFF
... SELECT ... END
Usually two SELECTIONS are defined. The first one is allowed to move and the second one serves at the interaction background to the first one. When only one selection is defined program assumes that the second one is equal to the first one.
Assumes that the SELECTIONS are already defined as KEYs. The first one as the KEY named ``active'' and the second as the KEY named ``passive''. These selection are usually defined through the interactive MENU items. See also MINIMIZE SELECT.
... BY CONJUGATED BODY
With CONJUGATED gradient MINIMIZATION (this is the default) the position of each atom from the first SELECTION is optimized separately, whereas using rigid BODY minimization the placement of the whole SELECTION as a single entity (GROUP) (rigid BODY) is optimized. The placement of POINTS in a map can be optimized only with the BODY method.
... STEP inte
The starting number of MINIMIZATION STEPS is 80.
... IMAGE_STEP inte
The IMAGE defines the number of MINIMIZATION STEPS after the molecular model IMAGE is redrawn (replaced with the new coordiates). The default value is 0, which means that the IMAGE is not updated during the MINIMIZATION. IMAGE is updated after the minimization is done. (This option is currently disabeled.)
... WRITE inte
With WRITE inte (5 is the default), the number of MINIMIZATION STEPS is defined after which the ENERGY summary is written to the terminal.
... LIST-GENERATION ON OFF
Turns ON/OFF the generation of lists for calculation of nonbonded energy terms (VDW and ELECTROSTATIC), ON is the default. The nonbonded interaction list generation considerably speedes up energy calculation, when the nonbonded energy terms are requested.
... PHASE ( STEPS inte MACRO file_name SELECT ... END FREE SELECT ... END KICK ( = real SEED inte LINEAR SQUARE EXPONENTIAL ) )
PHASE commands deal with structure factor and maps used in refinement.
Bra-kets can enclose a set of PHASE keywords. If you not use them you have to start from the command PHASE again to reach each additional PHASE keyword.
... STEPS inte
Zero is the default number, meaning rephasing is of, It is the number of MINIMIZATION steps after which a new structure factor set is calculated. The PHASE step number is meaningless unless the DENSITY ENERGY term is turned ON.
... SELECT ... END
Only the first selection (active) contributes to new map generation, the following structure factor calculation and difference map generation. (DENSITY MAP should be properly defined. See ENERGY DENSITY.) The second is used for "R-FREE" assesment.
... MACRO file_name
When PHASE MACRO is defined, then the new structure factors are to be calculated within that macro and not as by the default procedure. This is the way how to incorporate density modification procedures as well as various crystal form into a refinement procedure and thereby not break continuity of the gradient search by restarting it after each structure factor calculation. WARNING: You should, however, take care that the phasing and the difference map calculation make sense.
... KICK ( = real SEED inte LINEAR SQUARE EXPONENTIAL )
KICKING of structure factors during a refinement procedure results in convrgence problems of the refinement.
... SELECT ... END
Defines a selection of reflections that will be applied in R-FREE factor calculation. You must, however, take care that the reflections from this selection are not included in the selection used in refinement. See also MAIN_CMDS:refine.cmds, MAIN_DOC:refine/refine.html.
POSITION is the switch in a MINIMIZE command that turns the B-VALUE optimization off and turns the POSITIONAL optimization on.
This is the default.
... B-VALUES OVERALL INDIVIDUAL
B-VALUES turns the POSITIONAL optimization off and turns the B-VALUES optimization ON. POSITION optimization is the default. The B-VALUES flag has no effect when rigid BODY optimization is requested.
INDIVIDUAL B-VALUES are optimized for each defined GROUP. The smallest group can consist of one atom. See "DEFINE GROUP" and ENERGY B-VALUE commands.
OVERALL B-VALUE is optimized (actually calculated) on the basis of Wilson plot statistics.
> mininimize b-values overall sele ... end step 3
See also MAIN_DOC:refine/refine.html, define.html, energy.html.
... BASE = real
Sets the empty region of the unit cell to a specified value.
... RESCALE ON OFF
RESCALES the generated map before its Fourier transformation in order to introduce a real-space solvent correction. The default is OFF.
See also MAKE MAP RESCALE.