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Authors: Doug Collins and Jim Stewart Contact: Jim Stewart, Department of Chemistry, University of Maryland, College Park, MD 20742 USA MERUN takes in specifications for a MEDENS run to produce an initial direct space electron density map which is to be refined by MEFFIT. In the cycles of refinement the initial map is adjusted toward compliance with fixed structure moduli and the corresponding phase information is kept as calculated phases. During the cycles of refinement difference maps will be generated by the FOURR program and new calculated phases and moduli will be produced by RFOURR. Purpose MERUN sets up the XTAL input control lines required to run MEDENS followed by the requested number of cycles of RFOURR; FOURR; MEFFIT; followed by a final RFOURR. The main purpose is to simplify the multiple use of other Xtal programs and to automate, to a large extent, the I/O file switching. MERUN facilitates the process of extending and refining phases by the process of taking an initial electron density map and computing the constrained exponential electron density distribution for it by means of the program MEDENS. The output map may then be reverse Fourier transformed by the program RFOURR to produce structure factor phases and moduli corresponding to the maximum entropy map from MEDENS. From these moduli and phases and the observed structure factors it is possible to calculate a difference Fourier map using the program FOURR. This difference map and the original maximum entropy map are combined by use of the program MEFFIT to produce a modified maximum entropy map. This new map, when reverse Fourier transformed, will show moduli in better agreement with the observed moduli. If the initial phase set was of limited resolution, the resolution of each successive map will be higher at a rate dependent upon the acceptance criteria set for MEFFIT and RFOURR. In general several cycles will be required to achieve good agreement between the calculated and observed moduli and to expand fully their phasing and the resolution of the map. Method MERUN outputs line images to the line file aux. These images are either generated by default or may be passed through as model images from the MERUN input. The lines generated by MERUN may be automatically added to the Xtal input stream or may simply be printed for inspection. Printed Output It is possible to print the control lines from MERUN for inspection, but the main output will be that generated by the programs MEDENS, RFOURR, FOURR, and MEFFIT during the subsequent events. The output from these programs can be restricted by using the li option in the MERUN line. File Assignments Repeatedly reads the input archive bdf Repeatedly writes an output archive bdf Reads an electron density map from file map1 Repeatedly reads and writes map, med and mem files 1 Writes the final refined constrained exponential electron density map to
map1 1 Original map on the map file will be overwritten. Example This example run shows the generation of a low resolution electron density map from the saly test deck followed by a maximum entropy refinement and then by production of a final high resolution map. At the end a peak search and model building is done. FOURR fobs maxhkl 14 14 4 0.01 0.17857 :limit to 2.6 a resolution grid 35 35 15 :set high res for rfourr restrictns layout layer down across 35 35 15 0 0 0 1 1 1 PEKPIK :for interest's sake MERUN cy 3 sh 0.5 a 3.99 :generate all lines by default FOURR fobs :at full resolution now grid 35 35 15 layout layer down across 35 35 15 0 0 0 1 1 1 FOSTAT 20 1 -10 :optional for interest's sake PEKPIK MODEL limits 1 1.8 1.5 1.1 130 110 0 2 2.5 15 3 conect c1 c2 c6 c7 ; c2 c1 c3 o3 ; c3 c2 c4 ; c4 c3 c5 conect c5 c4 c6 ; c6 c5 c1 ; c7 o1 o2 The output file aux generated from the above input is shown below. TITLE READ A LOW RESOLUTION F OR E OBS FOURIER MAP FOR MEDENS PROCESSING remark READ FOBS FOURIER FROM .MAP WRITE MEDENS ON .MED medens SH 1.000 remark CALCULATE THE MAXIMUM ENTROPY DENSITY FUNCTION remark FOSTAT READS MEDENS MAP FROM .MAP COPYBDF MED MAP fostat 20 1 -10 TITLE CYCLE 1 TO SET PHASES AND F OBSERVED TO MAXIMUM ENTROPY DENSITY remark READ PREVIOUS MAXIMUM ENTROPY DENSITY FUNCTION MAP FROM .MAP rfourr FT 0.25 remark CYCLE 1 remark CALCULATE PHASES FROM THE MAX ENTROPY DENSITY MAP remark WRITE AN /FO-FC/ DIFFERENCE MAP ON .MAP fourr FDIF BLSUM NW remark CYCLE 1 remark CALCULATE A DIFFERENCE FOURIER USING THE EXTENDED PHASES remark THE DELTA F MAP USES THE MEDENS/MEFFIT PHASES grid 90 90 16 layout LAYER DOWN ACROSS 90 90 16 0 0 0 1 1 1 meffit A 3.990 remark CYCLE 1 remark MEDENS/MEFFIT FROM .MED DEL(F) .MAP NEW MEFFIT .MEM remark CORRECT THE MEDENS MAP TO CONTROL THE MAGNITUDE OF F OBS COPYBDF MEM MAP COPYBDF MEM MED TITLE CYCLE 2 TO SET PHASES AND F OBSERVED TO MAXIMUM ENTROPY DENSITY remark READ PREVIOUS MAXIMUM ENTROPY DENSITY FUNCTION MAP FROM .MAP rfourr FT 0.25 remark CYCLE 2 remark CALCULATE PHASES FROM THE MAX ENTROPY DENSITY MAP remark WRITE AN /FO-FC/ DIFFERENCE MAP ON .MAP fourr FDIF BLSUM NW remark CYCLE 2 remark CALCULATE A DIFFERENCE FOURIER USING THE EXTENDED PHASES remark THE DELTA F MAP USES THE MEDENS/MEFFIT PHASES grid 90 90 16 layout LAYER DOWN ACROSS 90 90 16 0 0 0 1 1 1 meffit A 3.990 remark CYCLE 2 remark MEDENS/MEFFIT FROM .MED DEL(F) .MAP NEW MEFFIT .MEM remark CORRECT THE MEDENS MAP TO CONTROL THE MAGNITUDE OF F OBS COPYBDF MEM MAP COPYBDF MEM MED TITLE CYCLE 3 TO SET PHASES AND F OBSERVED TO MAXIMUM ENTROPY DENSITY remark READ PREVIOUS MAXIMUM ENTROPY DENSITY FUNCTION MAP FROM .MAP rfourr FT 0.25 remark CYCLE 3 remark CALCULATE PHASES FROM THE MAX ENTROPY DENSITY MAP remark WRITE AN /FO-FC/ DIFFERENCE MAP ON .MAP fourr FDIF BLSUM NW remark CYCLE 3 remark CALCULATE A DIFFERENCE FOURIER USING THE EXTENDED PHASES remark THE DELTA F MAP USES THE MEDENS/MEFFIT PHASES grid 90 90 16 layout LAYER DOWN ACROSS 90 90 16 0 0 0 1 1 1 meffit A 3.990 remark CYCLE 3 remark MEDENS/MEFFIT FROM .MED DEL(F) .MAP NEW MEFFIT .MEM remark CORRECT THE MEDENS MAP TO CONTROL THE MAGNITUDE OF F OBS COPYBDF MEM MAP COPYBDF MEM MED TITLE AFTER 3 CYCLES CALCULATE PHASES FROM REFINED MAX ENT DENSITY MAP rfourr FT 0.25 remark CALCULATE PHASES FROM THE FINAL REFINED MAXIMUM ENTROPY DENSITY MAP |
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