2.11 *****************
* RD31 WRITE-UP *
*****************
RD31 is a program which reads the binary phase files output from
either PHASIT, BNDRY, GREF, MAPINV, MRGDF, MRGBDF or IMPORT and
converts it to a formatted file. The formatted file can be examined
and edited if desired, or it can be used to interface the current
phase information with other programs. Originally this program was
used to convert the binary file (generated on a Silicon Graphics IRIS
computer) to ASCII so that it can be transferred over an ethernet link
for use on a VAX. The program is interactive and prompts only for the
names of the input and output files. It can read both the "full" style
reflection records (includes probability distribution coefficients,
FOM etc), or the "short" style records produced by MAPINV, GREF, MRGDF
etc, and automatically determine which type was input. Program MK31B
can then be used to recreate the binary file from the output of this
program.
***** FILES *****
The input binary file should be the phased file output from PHASIT (in
protein phasing mode), BNDRY or IMPORT. It can also be the short phase
file output from GREF, MAPINV, MRGDF, MRGBDF or PHASIT (in structure
factor calculation mode, IHLCF=0).
The output ASCII file contains records with
H, K, L, FMFO, FO, PHIBEST, IPRAB, IPRCD, MK, FM
in FORMAT ( 3I4, 2F10.2, F7.2, 2I12, I5, F6.3 )
H,K,L = Miller indices
FMFO = Figure of merit weighted structure factor amplitude
(either FOM * FP or FOM * F+)
FO = Observed structure factor amplitude (either FP or F+)
PHIBEST = Best (centroid) phase, in degrees.
IPRAB Hendrickson-Lattman coefficients A,B,C,D for the phase
= probability distribution used, packed two per word as
IPRCD (IFIX(A*100)+16384)*32768 + IFIX(B*100)+16384 and
(IFIX(C*100)+16384)*32768 + IFIX(D*100)+16384
MK = Restricted phase indicator. For general reflections
MK=1, for centric reflections MK > 1 and one of the
allowed phase values is (MK-1)*15 degrees (the other
possibility is 180 degrees away).
FOM = Figure of merit associated with PHIBEST and used for
weighting.
If a file with "short" records was input, only the indices, F values
and phase are written in the output records.
2.12 ******************
* MK31B WRITE-UP *
******************
MK31B reads the ASCII version of the phase file created by RD31 and
creates a binary version. Both "full" or "short" files can be input,
and the program automatically determines which type was provided. See
RD31 section for details on the files. The program is interactive and
prompts only for the names of the input and output files.
2.13 ******************
* PSRCH WRITE-UP *
******************
PSRCH is a program which searches the map computed by FSFOUR and
lists the coordinates and heights for the largest peaks (positive
or negative). Only unique peaks will be listed. It has other options
useful in small molecule crystallographic applications, but for
protein work only the peak list is used, hence the other options are
bypassed and will not be described. This is essentially the peak
search program used in the MULTAN78 direct methods programming
package.
INPUT DATA (UNIT 5)
CARD 1 PAMFIL (free format)
PAMFIL = Name of input file containing cell parameters
and symmetry information (used only to get
running log file name).
CARD 2 MAPFIL (free format)
MAPFIL = Name of map file input.
CARD 3 NPEAK, NEGP (free format)
NPEAK = Number of largest peaks to list (Max=180)
= 0 gives the default of (11*n)/9 where n = number
of independent atoms (excluding H) as input to
FSFOUR
NEGP = 0 to list positive peaks, 1 to list negative
peaks
***** FILES *****
The input binary map file should be the output file from FSFOUR.
FSFOUR must have been run with the parameter NORN=0 specifying the XZ
section orientation.