MOLREP (CCP4: Supported Program)

NAME

molrep - automated program for molecular replacement

SYNOPSIS

molrep
[Keyworded input]

DESCRIPTION

For full details of MOLREP, see reference below, a copy of which is held in $CDOC/molrepdoc.rtf

INPUT AND OUTPUT FILES

The following input and output files are used by the program:

Input Files:

FILE_F
Reflection file containing observed amplitudes (MTZ, CIF or BLANC format)
FILE_M
Coordinate file containing search model (PDB or BLANC format)

Output Files:

molrep.doc
Log of run, if requested.
molrep.pdb
Coordinates of model, rotated and translated as appropriate.
molrep_rf.tab
List of solutions of rotation function.
molrep_rf.ps
Postscript file showing highest peaks in cross rotation function.

KEYWORDED INPUT

Program input is designed for interactive use, though it can be run via a script. The program queries whether you wish a FILE-DOCUMENT which is similar to a traditional log-file: 

  Do you want to have FILE-DOCUMENT /molrep.doc/ ? /<N>/Y/A :
    N - means without DOC-file
    Y - with new contents
    A - means to keep old contents and add new information
        with DOC-file program creates batch file: molrep.bat
Next the program asks for the name of the reflection file: 

 Input file with Fobs (format  ASCII (CIF or PDB) or BLANC or MTZ)
        Extention "dat" means BLANC file, extention "mtz" means MTZ file
If the input reflection file is in MTZ format, the program will prompt for column labels: 

 #     MTZ file keywords:
 #
 #F:        < >       - label of F or F(+)
 #SIGF:     < >       - label of sigma F or sigma F(+)
 #F-:       < >       - label of F(-)
 #SIGF-:    < >       - label of sigma F(-)
 #I:        < >       - label of I or I(+)
 #SIGI:     < >       - label of sigma I or  sigma I(+)
 #I-:       < >       - label of I(-)
 #SIGI-:    < >       - label of sigma I(-)
 #PH:       < >       - label of phases
 #FOM:      < >       - label of figure of merit

 # ---  type "key_word   parameters" and/or ---
 # ---  type "CR" for to run program        ---
 -->F: F
 -->SIGF: SIGF
Next the program will prompt for the name of the file containing the search model: 

 Input file with model (format PDB or BLANC)
 FILE_M: test_mod.pdb
And finally, the following keywords may be entered to control the fine behaviour of the program: 

 #
 #     Keywords for special cases:
 #
 #MODE:     <F>,S     - Fast or Slow
 #                      In Slow MODE advanced rotation and translation
 #                      functions and rigid body refinement are used.
 #                      In Fast MODE standard rotation and translation
 #                      functions are used without rigid body refinement
 #                      Fast MODE is much faster
 #RAD:   <automatic>  - cut-off radius for Patterson search.
 #                      Default for Self-RF : 30A
 #RESMAX:   <3>       - maximal resolution.
 #RES_R: <automatic>  - minimal resolution for Rotation Function
 #RES_T: <automatic>  - minimal resolution for Translation Function
 #                      Instead to apply RES_min program use
 #                      Boff=4*RES_min^2. Default: RES_R=15, BES_T - from model
 #BADD:     <0>         BOFF and BADD mean :
 #                      !F!new = !F!input *EXP(-BADD*RSQ)*(1-EXP(-BOFF*RSQ)
 #ANISO: <N>,Y,C,S    - Y anisothermal correction and scaling
 #                      C use anisothermal correction Fobs for RF
 #                      S use anisothermal scaling for TF
 #PACK:    <Y>,N      - use Packing Function with Translation Function
 #LMIN:    <4>        - miniimal L-index of sherical coefficients
 #LMAX: <automatic>,30,60 - maximal L-index of sherical coefficients
 #PST:  <N>,Y        - Y use pseudo-translation
 #VPST: <0,0,0>      - pseudo-translation vector (in fract)
 #                     default: automatically from Patterson
 #PRF:    <N>,Y      - Y means SAPTF and Phased Rotation Function will be used
 #PHASE: < >,+,-     - If you want to use phases from CIF or MTZ tape "+" or "-"
 #                     If you want to use the BLANC file of phase tape "+name"
 #                     or "-name". ("-" means inverted phases will be used)
 #ANGLES:  <0,0,0>   - rotation angles of model /only for FUN="T"/
 #LIST: <S>,L        - S - short DOC-file, L - long.
 #P2:     <0>        - experimental option, if P2 (percent of model_2) > 0
 #                     program uses !!Fobs!-!Fmod2!*(P2/100)! for RF
 #TEST: <N>,F,L,2    - please do not use it (for author only).
 #
 #   Without file of model program computes Self Rotation Function
 #
 #CHI:    <60>     - angle chi of additional 4th section of RF(thetA,phi,chi)
 #SCALE:  <6>      - maximal value of RF is SCALE * SIGMA(RF)
 #
 #          molrep_rf.ps - PostScript file of Self or Cross Rotation Function
 #
 #     Ordinary keywords:
 #
 #NP:    <10>      - number of peaks of rotation function to be checked.
 #                   Maximum: 50. Default: 10
 #NPT:   <20>      - number of peaks of translation function to be checked.
 #                   Maximum: 50. Default: 20
 #NMON:   <1>      - number of monomers. Program will try to create full model
 #COMPL:  <0>      - completeness of model: from 0.2 to 1.0. It corresponds
 #                   to Boff: from 400 to 1600. If COMPL is used keywords
 #                   RES_R,RES_T are ignored. Default: automatic choice
 #SIM:    <0>      - similarity of model: from 0.1 to 1.0 It corresponds
 #                   to Badd: from (B_limit-Boverall) to -Boverall,where
 #                   B_limit corresponds Optical Resolution. SIM=1 means
 #                   normalized F will be used. If SIM is used keywords
 #                   BADD is ignored. Default: Badd=0
 #                   SIM (Badd)   - controls high resolution data
 #                   COMPL (Boff) - controls low resolution data
 #FUN: <A>,R,L,T   - R  calc only Rotation Function
 #                   T  calc only Translation Function
 #                   L  calc only Translation Function, reading list of peaks
 #                      of RF from file: "molrep_rf.tab"
 #                   A  calc both: RF and TF
 #SURF: <N>,Y,A,O  - model correction: shift to the origin and :
 #                   Y - B = accessible surface area *10 + 15
 #                   A - polyalanine model and all B = 20
 #                   O - only shift
 #MODEL_2: filename - input file with the 2nd (fixed) model in the same
 #                    format as model_1 (PDB or BLANC). This model will
 #                    be fixed during the search. Default: no model_2
 #
 #       Output files:  (rotated & translated MODEL + MODEL_2):
 #                       molrep.crd  - if input FILE-MODEL in format BLANC
 #                       molrep.pdb  - if input FILE-MODEL in format PDB
 #                       molrep_rf.tab  - list of peaks of Rotation function
 #
When all necessary keywords have been given, carriage return starts the program.

EXAMPLES

Simple unix example script found in $CEXAM/unix/runnable/

SEE ALSO

amore
almn
polarrfn
tffc

REFERENCES

  1. A.A.Vagin and A.Teplyakov, J. Appl. Cryst., 30 1022 (1997)

AUTHORS

A.A.Vagin