molrep - descriptionMOLREP (CCP4: Supported Program)
NAME
molrep - automated program for molecular replacement
SYNOPSIS
molrep [HKLIN in.mtz] [MAPIN EM_map.ccp4] [MODEL in.pdb ( or EM_mod_map.ccp4)]
[MODEL2 in2.pdb] [PATH_OUT path_out] [PATH_SCR path_scr]
[Keyworded input]
DESCRIPTION
Version 7.3 /01.07.2002/
FEATURES
standard molecular replacement method by
cross rotation function (RF),
full-symmetry translation function (TF),
packing function (PF)
also
Self Rotation Function with PostScript plots
Spherically averaged phased translation function (SAPTF)
Phased Rotation(PRF)
Phased Translation functions (PTF)
Locked cross rotation function (LRF)
allows input of a priori knowledge of similarity and completeness of the
model.
scaling by Patterson origin peak
soft low resolution cut-off
anisotropic correction and scaling
can use modified stucture factors instead of Fobs for RF
rigid body refinement
can use second fixed model
if the number of monomers is known MOLREP can position the input
number of monomers in a simple run
can check and manage pseudo-translation
fitting two models
can just rotate and position the model and compute R-factor, CC
search model in electron density map
multi-copy searh
can choose from symmetry-related models closest to which was found before
can improve the model before use
model correction by sequence alignment
can use NMR model
can use EM or electron density map as model or use instead of Fobs
for searching a model in EM map
search model orientation in electron density map for particular position by
phased RF
find HA positions by MR solution
heavy atom search
CONTENTS
References
Input/output files
What MOLREP can do
How to use MOLREP
Keywords
Molecular replacement method. Some theory.
Command file examples
Convention for rotation and coord. system
Memory control parameters
REFERENCES
Author: A.A.Vagin
email: alexei@ysbl.york.ac.uk
References: A.A.Vagin, New translation and packing functions.,
Newsletter on protein crystallography., Daresbury
Laboratory, (1989) 24, pp 117-121.
Alexei Vagin and Alexei Teplyakov.
An approach to multi-copy search in molecular replacement.,
Acta Cryst.D,(2000) 56, pp 1622-1624
A.A.Vagin and M.N.Isupov
Spherically averaged phased translation function and
its application to the search for molecules and fragments
in electron-density maps
Acta Cryst.D,(2001) 57, pp 1451-1456
main: A.Vagin,A.Teplyakov, MOLREP: an automated program for
molecular replacement.,
J. Appl. Cryst. (1997) 30, 1022-1025.INPUT/OUTPUT FILES
Input file
HKLIN
Input MTZ file or CIFile structure factors
in the case of fitting two atomic models, leave this option out.
CIF file contains indices, structure factors (and phases if you need them):
h,k,l,|F|,sig(F),Phi or h,k,l,|F|,sig(F),Phi,Fom
MTZ file must have extension "mtz".
MAPIN
MAPIN can be used instead of HKLIN
Input file with CCP4 map.
EM or electron density file in CCP4 format (File must have extension "ccp4").
This file will be converted to files of !F! and phases.
In the case of fitting two atomic models, leave this option out.
MODEL
Input PDB file with the coordinates or CCP4 map.
(CCP4 map file must have extension "ccp4").
Without this file the program computes a Self Rotation Function and plots
RF(theta,phi,chi) for
chi = 180, 90, 120, 60
You can change the fourth value of chi (60) by keyword CHI
You can change the scale of these plots of RF by keyword SCALE
MODEL2
Input PDB file with second fixed model
PATH_SCR
You can use this variable to redirect all scratch files to special directory.
Default is value of TEMP1 or CCP4_SCR variable.
If 'PATH_SCR .' all scratch files will be in current directory.
PATH_OUT
You can use this variable to redirect output files to special directory.
Space group and unit cell parameters of the unknown structure will be taken from
the file of structure factors. You can change the space group of the structure
factor file by using keyword NOSG.
Output files
molrep.pdb
new PDB coordinate file of model (plus model_2) corresponding to the best
solution of Cross Rotation and Translation Function.
molrep_fcalc.cif
formatted CIFile of molrep solution (plus from model_2) with Fobs, Fcalc,
Phcalc (this files will be created if your model is EM or density in CCP4
format).
molrep.doc
additional protocol (like log file in CCP4). This file will be created if
keyword DOC is 'Y' or 'A'.
molrep_rf.tab
List of peaks of rotation function, created as soon as the program calculates
a Rotation Function.
molrep_rf.tab is default name, you can use another name using keyword FILE_T.
You can edit this file and use it for subsequent calculations without
computing the rotation function again (keyword FUN=T). The program then reads
(in free format!): "Sol_", peak number and Polar angles (theta,phi,chi), e.g.:
"Sol_ 23 10.0 22.2 40.0"In 'Rotation and Position the model' (keyword FUN=S), the program reads
"Sol_", peak number,Polar angles and shift (sx,sy,sz) e.g.:
"Sol_ 23 10.0 22.2 40.0 .564 .443 .032"If you like to use Eiler angles use "Sol_A" instead "Sol_"
In 'Search model orientation by PRF' (keyword PRF=P), the program reads
"Sol_", peak number,Polar angles and shift (sx,sy,sz) e.g.:
"Sol_ 23 10.0 22.2 40.0 .564 .443 .032"But program will use only the shift (sx,sy,sz).
molrep_srf.tab
List of peaks of Self Rotation Function.
molrep_srf.tab is default name, you can use another name using keyword
FILE_TSR.
molrep_rf.ps
PostScript file of Self Rotation Function
also (if you used keyword FILE_S):
align.pdb
input model corrected by sequence alignment
WHAT MOLREP CAN DO
+-- Self RF (FUN=R, without any model)
!
+-- Standard MR -+-- Cross RF (FUN=A or FUN=R )
! !
! +-- Locked Cross RF ( FUN=A or R and LOCK=Y )
! !
! +-- TF (FUN=A or FUN=T )
!
!
! +- two identical models
! !
! +-- Dyad search -+
! ! (DYAD=D) !
+-- Multi-copy search -+ +- two different
! for MR ! models
! !
MOLREP --+ +-- Multy-copy for one model
! (DYAD=Y)
!
!
! +-- RF and PTF
! ! (PRF=N)
! !
+-- Fitting two models -+-- SAPTF, RF and PTF
! ! (PRF=S)
! !
! +-- SAPTF, PRF and PTF
! (PRF=Y)
!
!
! +-- RF and PTF
! ! (PRF=N)
! !
+-- Searching in ED map -+-- SAPTF, RF and PTF
! ! (PRF=S)
! !
! +-- SAPTF, PRF and PTF
! (PRF=Y)
!
+-- Rotate and position the model (FUN=S FILE_T)
!
!
!
+-- Search model orientation in electron density map
! for particular position by phased RF (PRF=P FILE_T)
!
!
! +-- find HA positions by MR solution
! ! (FUN=D, model_2)
! !
+-- HA search ---+-- HA search for SIR or SAD
! ! (DIFF=H, FUN=T, without any model)
! !
! +-- Self RF for HA position
! (DIFF=H, FUN=R, without any model)
!
+-- pure RB refinement (in patterson or real space, FUN=B, model_2)
where: FUN, DYAD, PRF, LOCK, DIFF - keywords
MR - Molecular Replacement
RF - Rotation function
TF - Translation function
PRF - Phased Rotation function
PTF - Phased Translation function
SAPTF - Spherically Averaged Phased Translation function
ED - Electron density
HA - heavy atom
RB - rigid body
Standard molecular replacement method
Self Rotation Function only
Search model in electron density map
Search model orientation by PRF
Fitting two models
Just rotate and position the model
Multi-copy search
Model correction
Use sequence alignment
NMR model
EM or electron density model
Locked Cross Rotation Function
rigid body refinement
* Standard molecular replacement method
The program performs molecular replacement in two steps:
Rotation function (RF)
search orientation of model
Cross Translation function (TF) and Packing function (PF)
search position of oriented model
The result of the Rotation function depends on the radius of a spherical domain
in the centre of the Patterson function (the so-called cut-off radius). This
radius must be chosen so as to maximize the ratio between the number of inter-
and intramolecular vectors. The program chooses the value of this radius as
twice the radius of gyration, but can also use an input value.
Instead of computing RF, the program can use a list of orientations from a
Rotation function (keyword FILE_T) which was prepared before. Anisotropic
correction of data before computing RF can be useful for data with high
anisotropy (keyword ANISO).
With a second fixed model, the use of modified stucture factors instead of
|Fobs| for RF (keyword DIFF) may make RF clearer. The modified stucture factor
is:
||Fobs|-|Fmod2|*(P2/100)|
where P2 is the percentage of model_2 in the whole structure.
The Translation function can check several peaks of the rotation function by
computing a correlation coefficient for each peak and sorting the result. For
scaling observed and calculated structure factors, the program uses the scaling
by the origin peak of Patterson, but for data with high anisotropy the program
can use anisotropic scaling. The Translation function can take into account the
second fixed model and also, if the number of monomers is known, MOLREP can
position the input number of monomers in a simple run (keyword NMON). Also in
this case the possibility to choose from symmetry-related models closest to
which was found before is useful (keyword STICK).
The program can detect and use pseudo-translation vectors. In this case the
pseudo-translation related copy will be added to the final model (keyword PST).
The Packing function is very important in removing wrong solutions which
correspond to overlapping symmetry-related or different models (keyword PACK).
Use keywords:
COMPL, DIFF, FUN, NMON, NP, NPT, P2, PACK, PST, RAD, RESMAX, SIM, STICK, SURF,
VPST, NREF, NREFP, FILE_T, FILE_TSR, NSRF
* Self Rotation Function only
If you define only a file of structure factors (Fobs), the program will compute
a Self Rotation function with cut-off radius RAD = 30 as default. Use keyword
RAD if you want another value. Other useful keywords: RESMAX, RES_R, COMPL, SIM.
Resulting output:
molrep_srf.tab
List of peaks of Self Rotation Function.
molrep_srf.tab is default name, you can use another name using keyword
FILE_TSR.
molrep_rf.ps
PostScript file of Self Rotation Function which contains four plots RF
(theta,phi,chi) for
chi = 180, 90, 120, 60.
You can change the fourth value of chi (60) by keyword CHI
You can change the scale of these plots of RF by keyword SCALE
* Search model in electron density map
In some cases it is difficult to solve an X-ray structure by molecular
replacement even when a structure for a homologous molecule is khown. If prior
phase information either from SIR/MAD or from a partial structure is known, this
could be used in a six-dimensional search. The program divides the
six-dimensional search with phases into three steps:
a spherically averaged phased translation function (SAPTF) is used to locate
the position of the molecule or its fragment. It compares locally spherically
avaraged experimental electron density with that calculated from the model and
tabulates highest scoring positions.
then for each such position a local phased rotation function (PRF) is used to
find the orientation of the molecule.
Another possibility is to use usual rotation function (RF) for modified map,
i.e program sets 0 the density outside of sphere with radius = twice radius of
model and with the centre in current point.
the phased translation function (PTF) for found orientation which checks and
refines the found position.
You need to have the phases in a CIF file of structure factors or to use
corresponding keywords for MTZ file or use EM map as input instead of Fobs file.
with keyword PRF = 'N' (default value):
usual Rotation function and Phased Translation function will be used.
with keyword PRF = 'Y':
SAPTF (Spherically averaged phased translation function), Phased Rotation
function and Phased Translation functions will be used.
with keyword PRF = 'S':
1.SAPTF (Spherically averaged phased translation function). 2.For current
point of SAPTF solution input map is modified, i.e program sets 0 the
density outside of sphere with radius = twice radius of model and with the
centre in current point. 3.usual Rotation function for this modified map.
4.Phased Translation functions
Other useful keywords:
COMPL, NMON, NP, NPT, RAD, RESMAX, SIM, SURF, INVER
Also you can refine solution by Pure Rigid Body Refinement
* Search model orientation in electron density map for particular position by
PRF
You can use this possibility (keywords PRF=P and FUN=R or A) if you want to find
the model orientation in ED map by rotating model around the defined point in ED
map. Program puts the origin of model coordinate sysytem to the defined point
and performs phased rotation function (PRF). Use keyword RAD to define the
radius of sphere for PRF.
You must define the list of defined points of ED map using file FILE_T , wich
must contain lines with "Sol_", peak number,Polar angles and shift (sx,sy,sz)
e.g.:
"Sol_ 23 10.0 22.2 40.0 .564 .443 .032"But program will use only the shift (sx,sy,sz).
Model is rotated around the origin of model coordinate sysytem. If keyword SURF=
Y,A,2,O program puts the centre of model to the origin of model coordinate
sysytem automatically. If you want, for example, to rotate the model around some
atom, shift the origin to this atom and use SURF=N
Other useful keywords:
COMPL, NMON, NP, NPT, RESMAX, SIM, INVER
* Fitting two models (FM)
The idea is to fit the electron densities instead of the atomic models, trying
to find the best overlap. Advantages are:
can be used for cases with very low homology;
can be used when amino acid sequence is absent;
no need to use the list of equivalent atoms.
If you define only two files of models (searching model and model_2), without a
file of structure factors (HKLIN), the program will fit the search model (MODEL)
to the second model (MODEL2). The search model must be smaller or equal to the
second model.
with keyword PRF = 'N' (default value):
usual Rotation function (RF) to search the orientation and Phased
Translation function (PTF) to search position will be used.
with keyword PRF = 'Y':
Spherically averaged phased translation function (SAPTF) gives the expected
position for model. Phased Rotation function (PRF) for expected position
gives orientation. Phased Translation function (PTF) checks and refines the
translation vector.
with keyword PRF = 'S':
see above Search model in electron density map
Other useful keywords:
COMPL, NP, NPT, RAD, RESMAX, SIM, SURF
The result is file molrep.pdb - model fitted to second model.
* Just rotate and position the model
This possibility may be useful if you want to place the model to a particular
orientation and position, or to compare several solutions.
Use keyword FUN=S and define three files: a model (MODEL), a file of structure
factors (HKLIN) and file with polar angles and shifts (keyword FILE_T). The
program will shift the model to the origin, rotate (by polar angles) and the
position it (in fractional unis). The new model will be written to an output
coordinate file. Also the program will compute an R-factor and a Correlation
Coefficient.
Other useful keywords:
COMPL, RESMAX, RES_T, SIM
* Multi-copy search
There are two modes: "dyad_search" and "Multi-copy search".
Dyad_search - Search two copies of a model simultaneously (keyword DYAD=D).
Sometimes you can not find a solution starting with one molecule if you have
several copies of the molecule in the asymmetrical part of the unit cell. In
this case a search with two independent molecules may give a solution. The
central point of method is the construction of a multi-copy search model from
properly oriented monomers using a special TF (STF), which gives the
intermolrecular verctor between properly oriented monomers (dyad). This dyad can
then be used for a positional search with a conventional TF.
the program checks all pairs of NP peaks of the Rotation Function (RF). For
each pair the program uses the first rotation to prepare model-1. Model-2 will
be prepared by using the second rotation and one rotation from the
crystallographical symmetry operators. The total number of pairs to be checked
is ((NP+1)*NP*Nsym)/2
next, for model-1 and model-2: the program computes the Special Translation
Function ( STF) to find the inter-molecular vector of the dyad.
for NPT peaks (i.e. inter-molecular vectors) of the STF, the program computes
the standard Translation Function (TF) using the current dyad as a model, and
it calculates a Correlation Coefficient for the firstNPTD peaks of the TF.
Solution and output file: molrep.pdb will be the dyad with the best Correlation
Coefficient (or several dyads if keyword NMON > 1).
WARNING: the procedure takes quite some time, because the total number of
Translation Functions to be calculated is NMON*NPT*((NP+1)*NP*Nsym)/2.
In the output .log (.doc) file you can find the following information:
Sol_ R1 R2 Rs Rslf STF TF Shift_1 PFmax PFmin Rfac Corr
Sol_ 1 1 1 0 2 1 0.059 0.000 0.201 1.01 0.99 0.569 0.379
and
Sol_best 1 1 1 0 2 1 0.059 0.000 0.201 1.01 0.99 0.569 0.379
Sol_best Rot1-->2 Dyad_vector dist d_ort d_par
Sol_best 0.0 0.0 0.0 -0.210 0.000 -0.487 39.2 19.6 33.9
These lines means:
R1
peak number of rotation for model-1
R2
peak number of rotation for model-2
Rs
CS operator number which applyed before rotation for model-2
Rslf
peak number of self rotation function
STF
peak number of special translation function
TF
peak number of translation function
Shift_1
position of model-1
PFmax PFmin
min, max values of Packing function
Rfac Corr
R-factor and Correlation Coefficient
Rot1->2
polar angles of rotation from model-1 to model-2.
Dyad_vector
vector (in fractional) from model-1 to model-2.
dist d_ort d_part
first number - distance between models (in Angstrom)
second number - distance orthogonal to rotation 1->2
third number - distance parallel to rotation, i.e. for pure dimer this is 0.
With keyword LIST=L you can find additional information:
Sol_ angles_1 angles_2 shift_2
Sol_ 90.63 98.70 118.12 90.63 98.70 118.12 0.189 0.256 -0.415
+---------------------------------------------------------+
! !
! !
! !
! !
! !
! ----------------- ----------------- !
! / \ / \ !
! / \ / \ !
! ! rotated (angles_1) ! ! rotated (angles_2) ! !
! ! monomer_1 ! ! monomer_2 ! !
! ! ! dyad ! ! !
! ! +----------!-----------------+ ! !
! ! / ! vector! ' ! !
! ! / / \ ' / !
! \ / / \ / !
! \ / / ' \ / !
! ---/------------ ' -------------- !
! /shift_1 ' shift_2 !
! / ' !
! / ' !
! / ' !
! / ' !
! / ' !
! / ' !
! / ' !
!/ ' !
+---------------------------------------------------------+
origin
If you believe the Self-RF, you can try to find a dyad which has the rotation
between monomers corresponding to the rotation of the Self-RF (use keywords
NSRF,FILE_TSR).
Model-2 can be different from model-1. Use keywords FILE_M2 to define file of
searching model-2, FILE_T2 with list of peaks rotation function for this model
(this RF have to be computed before) and NP2 number of peacks which will be
used.
Multi-copy search - Search many copies of a model (not only dyad) (keyword
DYAD=Y). Program starts to search a single monomer, after that produces the dyad
search, repeates dyad search for next dyad with the first being fixed and
,finaly, tryes add a single monomer.
Use keywords:
DYAD, DIST, NP, NSRF, NPT, NPTD, NP2, AXIS, FILE_M2, FILE_T2, FILE_T,
FILE_TSR, NMON, ALL, PACK
and also:
COMPL, SIM, RESMAX, SURF, STICK
* Model correction
You can improve your model beforehand by using keyword SURF.
* Using sequence alignment
Another way to improve your model is to use the sequence of the unknown
structure.
Use keyword FILE_S to define a file containing a sequence. This sequence file
must be ASCII:
!
!
!# sequence
!SVIGSDDRTRVTNTTAYPYRAIVHISSSIGSCTGWMIGPKTVATAGHCIY
!# this is comment
! DTSSG--SFAGTATVSP GRNGTSYPYG
!NRGTRITKEVFDNLTNWKNSAQ!
If the first symbol in the line is "#", it means the line contains comments.
Blancs are ignored.
The program will perform sequence alignment and create a new corrected model
with the atoms corresponding to the alignment. The output file with the
corrected model is align.pdb. The results of the alignment are written to the
DOC-file, if this was defined. Without an Fobs file, the program only performs
model correction.
* NMR Model
You can use PDB file with NMR models or pseudo-NMR file with several homologous
structures which were superimposed before. Algorithm is equivalent to sum RF
or/and TF for individual structures. Program can find the best model in NMR file
or use all models (see keyword NMR) .
In the PDB file different models must be separated by MODEL record. For example:
HEADER HYDROLASE (ENDORIBONUCLEASE)
CRYST1 64.900 78.320 38.790 90.00 90.00 ...
MODEL 1
ATOM 1 N ASP A 1 45.161 12.836 ...
ATOM 2 CA ASP A 1 45.220 12.435 ...
...
ATOM 745 SG CYS A 96 58.398 6.673 ...
ATOM 746 OXT CYS A 96 62.238 7.178 ...
ENDMDL
MODEL 2
ATOM 1 N ASP B 1 44.487 11.386 ...
ATOM 2 CA ASP B 1 44.559 11.129 ...
...
Use keyword NMR
* EM or electron density model
Searching model can be Electron Microscopic model (EM) or electron density map.
Only values higher the limit (if keyword ROLIM is defined) will be used. Map
must have space group P1 and contains whole model. Vector ORIGIN defines the
centre of model and the rotation will be performed around this point. If
parameter DRAD (radius of model) is defined program will use the density only
inside the sphere with radius = DRAD and with centre in vector ORIGIN.
+--------------------------------+ nz
! ! !
! . .
!
! ! !
! . .
!
! ! !
! +--------------------------------+ izmax
! ! !
! ! !
! ! !
! ! ---------------- !
! ! / \ !
! ! / \ !
! ! / \ !
C_cell ! / \ !
! ! ! ! !
! ! ! DRAD ! !
! ! !---------- + ! !
! ! ! / centre ! !
! ! ! / / !
! ! \ / / !
! ! \ / / !
! ! \ / / !
! ! \ / / !
! ! -/-------------- !
! ! / !
! ! / !
! ! / ORIGIN !
! ! / !
! ! / !
! ! / !
! !/ !
! +--------------------------------+
0 nx
----------- A_cell --------------
Program will get vector ORIGIN from file automatically. If it is not possible to
get correct vector, program will use ORIGIN = ( 0.5, 0.5, izmax/(2*nz)). If you
want you can define ORIGIN yourself.
Use keywords:
DSCALEM, INVERM, ROLIM, DRAD, ORIGIN
Also you can use EM or electron density map instead of file of Fobs. In this
case map will be converted into !F! and phases and
Search model in electron density map will be performed as usual.
Use keywords:
DSCALE, INVER, DLIM
* Locked Cross Rrotation Function
Locked Cross Rotation function (LRF) means to average the Cross Rotation
function by NCS which can be determined with Self Rotation function. LRF is
especially useful when NCS forms a group.
Use keywords:
LOCK, NSRF, FILE_TSR,
* Rigid body refinement
If keyword MODE = S program produces Rigid Body refinement for each peak of TF.
Number of cycles is controled by keyword NREF (default 10). Also program can
refine the orientation given by RF before TF. In this case program produces
Rigid Body refinement (in space group P1) for each peak of RF. Number of cycles
is controled by keyword NREFP. Default value is 0, i.e. without this refinement.
Use keywords:
MODE, NREF, NREFP
If your model contains several domains you can use multi-domain Rigid body
refinement. For this you must put into PDB file additional lines before each
domain. Additional line contains word '#DOMAIN' and number of domain (free
format).
For example:
HEADER HYDROLASE (ENDORIBONUCLEASE)
CRYST1 64.900 78.320 38.790 90.00 90.00 ...
#DOMAIN 1
ATOM 1 N ASP A 1 45.161 12.836 ...
ATOM 2 CA ASP A 1 45.220 12.435 ...
...
ATOM 745 SG CYS A 96 58.398 6.673 ...
ATOM 746 O CYS A 96 62.238 7.178 ...
#DOMAIN 2
ATOM 747 N PHE A 97 44.487 11.386 ...
ATOM 748 CA PHE A 97 44.559 11.129 ...
...
ATOM 945 C VAL A 196 58.398 6.673 ...
ATOM 946 O VAL A 196 62.238 7.178 ...
#DOMAIN 1
ATOM 947 N ASP A 197 44.487 11.386 ...
ATOM 948 CA ASP A 197 44.559 11.129 ...
...
Also you can use Pure Rigid Body Refinement in Patterson or Real space. This
possibility is useful in the last stage of MR. For example after fitting the
model into EM map. If you want to use multi-domain Rigid body refinement define
domain structure in PDB file (see above) and use keyword DOM = 'Y'.
Use keywords:
FUN = B, DOM, NREF
* Find HA positions by MR solution
Use keywords:
FUN = D, MODEL_2,
* Heavy atom search
In this case you need not to use any model.
Use keywords:
DIFF = H, FUN = T or R,
'FUN = T' means Heavy atom search (experimental version)
'FUN = R' means Self RF for Heave atom structure.
HOW TO USE MOLREP
A simple way to use MOLREP is to define files for Fobs (HKLIN) and the model
(MODEL), number of model to search (keyword NMON), and use default values for
all parameters (i.e. without using any keywords). There is always a chance of
solving the structure automatically. If this does not work, use a common
strategy of molecular replacement.
Planning ahead
Success of the molecular replacement method depends on:
quality of experimental data
scaling |F|_obs and |F|_calc
low resolution limit
high resolution limit
quality of the model, homology, conformation
Things to look out for:
data
Look at your data quality. Completeness is very important. Absence of low
resolution reflections may cause problems, especially if the model is some
part of a whole structure. Look at anisotropy and twinning.
Think carefully: can you 'safely' use the high resolution reflections? If not,
use keyword SIM to remove the potentially bad effect of this part of the data.
It might be a good idea to use some program to check the data, for example
SFCHECK
model
Look at the model regarding the shape. The automatic choice of the cut-off
radius for RF is twice the radius of gyration. This is good enough if the
shape is approximately spherical. If the model is very asymmetrical, it is
better to make a choice yourself. Remove from your model the heavy atoms and
some terminal residues if they lie 'outside' the model.
Make a choice for SIM,COMPL. If you have not any idea about similarity,
SIM=0.5 is a good approximation.
If you have a dimer use it, but use RAD corresponding to a monomer.
It is very useful to shift the model to the origin of coordinates. Use keyword
SURF = O or Y (Y is default).
Self-RF
Compute Self-RF. It may give you some idea about NCS or about the number of
copies in the asymmetrical part of unit cell. Choose the radius of integration
carefully. The program can not make any informed choice about it without a
model (default is 30Å).
Cross-RF only
Compute Cross-RF with LIST=L and DOC = Y. In the DOC_file you can find the
list of expected orientations of the model and also the rotations between
them. Compare this with the Self-RF. This is an additional check of
correctness of the expected orientation. But sometimes we can not find
corresponding peaks in Self-RF for correct orientation.
If you have high anisotropy in the data, use anisotropic correction.
Translation function
If there are several copies of the model in the asymmetrical part of unit
cell, use keyword NMON or multi-copy or dyad search. You can not use the
option of Pseudo-translation for a dyad search, since this can recognize
Pseudo-translation itself.
If you have high anisotropy in the data, use anisotropic scaling.
Pseudo-translation
MOLREP can detect pseudo-translation, and define a pseudo-translation vector.
If keyword PST = Y, the program applies pseudo-translation with a
pseudo-translation vector which was defined by the program or the user. When
calculating a Translation Function, the program will use this vector to modify
structure factors. Pseudo-translation copy will be added to the final model at
the end program running.
If FUN=R and LIST=L MOLREP computes a list of Patterson peaks and writes these
to molrep.doc. This may be helpful in the detection of pseudo-translation.
Use keywords:
PST, VPST
Flexible model
If your model is flexible, for example, consists of two domains, you can try to
solve this problem by two ways:
1. Create two files for each domain and use dyad search (DYAD = D)
2. Combine these two domain files to single file with line "MODEL" between
domains (like NMR file). Use usual Molecular Replacement methods with keyword
NREFP or MODE = S and NREFP.
The use many homologous models
If you have several homologous models you can create a pseudo NMR file with
these models and use its together (see NMR model). But these models must be
superimposed before, for example, by MOLREP (see fitting two models).
Keep in mind
If you want to play with parameters, use also Keywords for special cases.
Without a model file, the program only computes a Self Rotation Function.
Model correction can be performed by using keyword SURF, or by including
FILE_S, a file with a sequence for sequence alignment.
If FUN=R, the program computes and writes to molrep.doc all symmetry-related
peaks of the Rotation Function. If also keywords NSRF and FILT_TSR are used
you can fine the pairs of peaks of cross RF which corresponds to NCsymmetry.
If you want to change the space group of the structure factor file, use
keyword NOSG, i.e. new space group number.
The Packing Function (PF) is very important to remove wrong solutions which
correspond to overlapping symmetry-related or different models. But you can
remove this option (PACK = N ), for example, if you want to find the model in
a special position. Value of PF = 1 corresponds to non-overlapping, value = -1
corresponds to completely overlapping two models.
When MOLREP is trying to find several models (NMON > 1) it is useful to use
keyword STICK = Y. Then for each additional molecule the program will choose a
symmetry-related molecule closest to which was/were found before. This option
does not work with pseudo-translation.
Do not use MODE = S without serious consideration.
For the PRF and the SAPTF, the default cut-off radius is once the radius of
gyration, whereas for a Patterson calculation the cut-off radius would be
twice the radius of gyration.
KEYWORDED INPUT
The available keywords are:
General keywords
Common:
DOC, LABIN, FILE_T, FUN, NMON, NP, NPT, RAD PATH_SCR
And for structure factors control:
COMPL, RESMAX, SIM
And for model control:
SURF
And for multi-copy search:
DYAD, FILE_M2, FILE_T2, NP2, NPTD, NSRF
And for search in ED:
PRF, INVER
And for fitting two models:
PRF
And for EM or electron density model:
DSCALEM, INVERM, ROLIM, DRAD, ORIGIN
And for EM or electron density instead of Fobs:
DSCALE, INVER, DLIM
Keywords for special cases
Common:
ANISO, BADD, LIST, LMAX, LMIN, MODE, PACK, RES_R, RES_T
And for standard MR:
DIFF, FILE_S, NMR, NOSG, P2, PST, STICK, VPST, LOCK, NREF, NREFP
And for Self RF:
CHI, PST, SCALE, FILE_TSR
And for multi-copy search:
AXIS, DIFF, DIST, P2, ALL, STICK
And for search in ED:
DIFF, P2, NPTD
And for fitting two models:
NPTD
And for Pure Rigid Body Refinement:
DOM
General keywords
LABIN =...
Specify input column lables.
The program labels defined are: F, SIGF, F(-), SIGF(-), I,SIGI, I(-), SIGI(-),
PHIC, FOM
Flabel of F or F(+)
SIGFlabel of sigma F or sigma F(+)
F(-)label of F(-)
SIGF(-)label of sigma F(-)
IStructure Intensity of hkl
SIGIStandard deviation of the above
I(-)Structure Intensity of -h -k -l
SIGI(-)Standard deviation of the above
PHlabel of phases
FOMlabel of figure of merit
DOC < N | Y | A >
Default:
use the additional file with the protocol of the running of the program:
DOC-file molrep.doc
Ndo not produce DOC-file
Yproduce DOC-file with new contents
Akeep old contents and add new information, i.e. if a file molrep.doc
already exists, the program will add any new information to the end of
this file
The DOC-file contains the protocol of the running of the program.
NP
Default: <10>
is the number of peaks from the rotation function to be used/checked
(maximum: 50).
In special cases (e.g. for a dyad search), the use of keywords FUN (with option
'T') and FILE_T is closely linked to NP.
NPT
Default: <20>
is the number of peaks from the translation function to be used/checked
(maximum: 50).
For use in dyad search, see NPT for dyad search.
NMON
Default: <1>
is the number of monomers. The program will try to create a full model,
which will consist of NMON initial models plus model_2.
COMPL
Default: automatic choice
is the completeness of the model: from 0.1 to 1.0. It corresponds to
Boff: from RESMAX*2 to RESMAX*6. If COMPL is used, keywords RES_R and RES_T are
ignored.
For example: if you have a dimer in the asymmetric part of the unit cell,
COMPL=0.5.
SIM
Default: automatic choice
Similarity of the model: from 0.1 to 1.0. It corresponds to Badd: from Boverall
to -Boverall. SIM=1 means normalized F will be used. When no knowledge of
similarity is available, the use of SIM=0.5 as a starting value is recommended.
If SIM is used, the keyword BADD is ignored.
SIM (Badd)
controls high resolution data
COMPL (Boff)
controls low resolution data
The use of Boff and Badd means to change Fobs and Fmodel:
|F|_new = |F|_input *exp(-Badd*s2)*(1-exp(-Boff*s2)
FUN < A | R | T | S | B | D >
Default:
Rcalculate only Rotation Function
Tcalculate only Translation Function, reading list of peaks of RF from
file (molrep_rf.tab) or from TAB_file
Acalculate both: RF and TF
Srotate and position the model and compute R-factor and Correlation
Coefficient
Bpure Rigid Body refinement
Dfind HA positions by MR solution
FILE_T
Default:
Input or output TAB_file (see also molrep_rf.tab)
SURF < N | Y | A | O | 2 >
Default:
Perform model correction.
Ndo not perform any model correction.For FUN=S (just_rotate_and_position)
program changes N to O
Oonly shift to the origin
Amake the protein into a polyalanine model (i.e. remove from the model:
water molecules, H atoms, atoms with alternative conformation (except the
first), atoms with occupacy = 0), make all B = 20, and shift to the origin
Yremove various atoms from the model (water molecules, H atoms, atoms with
alternative conformation (except the first), atoms atoms with occupacy =
0), shift to the origin, compute atomic accessible surface area and
replace atomic B with B = 15.0 + SURFACE_AREA*10.0
2set all B = 20 and shift to the origin
RAD
Default: automatically calculated from the model, unless:
in case of Self-RF calculations: 30Å
for Rotation Function calculations: twice the radius of gyration
for PRF and SAPTF: radius of gyration
Cut-off radius for Patterson search or for electron density search.
RESMAX
Default: <3>
High resolution limit.
Keywords for special cases
PST < N | Y | C >
Default:
How to deal with pseudo-translation.
Nignore pseudo-translation altogether
Ccheck only, but do not use pseudo-translation If FUN=R and LIST=L, the
program computes a list of Patterson peaks and writes these to
'molrep.doc'. It may be useful to detect pseudo-translation.
Yuse pseudo-translation. For the Translation Function, the program will
add to the model a copy of the model which is translated by the
pseudo-translation vector.
VPST
Default: automatically from Patterson
Pseudo-translation vector (in fractional units), used when PST = Y.
MODE
Default:
Fstandard rotation and translation functions are used without rigid body
refinement
Sadvanced rotation and translation functions and rigid body refinement are
used
Mstandard rotation and translation functions are used. Rigid body
refinement is possible. Rather slow then MODE=F, but correlation
coefficient is calculated more correctly.
RES_R
Default: automatic choice
Low resolution limit for Rotation Function. Instead of applying RES_R directly,
the program uses all data and applies Boff=4*(RES_R)2.
RES_T
Default: automatic choice
Low resolution limit for Translation Function. Instead of applying RES_T
directly, the program uses all data and applies Boff=4*(RES_T)2.
BADD
Default: <0>
BOFF and BADD mean:
|F|_new = |F|_input *exp(-Badd*s2)*(1-exp(-Boff*s2)
ANISO < N | Y | C | S | K >
Default:
Ndo not use anisotropic correction and/or scaling
Yuse anisotropic correction and scaling
Cuse anisotropic correction of Fobs for RF only
Suse anisotropic scaling for TF only
Kuse scaling without B-factor
PACK < Y | N >
Default:
Yuse Packing Function with Translation Function
Ndo not use Packing Function with Translation Function
LMIN
Default: <4>
Minimum L-index of spherical coefficients. The program does not use coefficients
with L=0. Possible values are 2,4,6,... L = 2 means to use all coefficients up
to Lmax.
LMAX
Default: automatic choice
Maximum L-index of spherical coefficients. Possible values are
2,4,6,8,...,58,60.
PRF < N | Y | S | P >
Default:
Nstandard RF and Phased Translation Function is calculated
YSAPTF (Spherically averaged phased translation function), Phased Rotation
Function (PRF) and Phased Translation Function will be used.
SSAPTF (Spherically averaged phased translation function), Usual Rotation
Function (RF) for modified map and Phased Translation Function will be
used.
PSearch the model orientation in ED map by rotating model around the
defined points in ED map. List of points must be in the file FILE_T.
Program will use the phases from MTZ file or from EM map.
If keyword FUN=T, rather than computing the Rotation Function, the program reads
rotation function results from file FILE_T ( or "molrep_rf.tab"): "Sol_ peak
number, polar angles (theta,phi,chi) and shift (sx,sy,sz)"
NOSG
Default: <0>
Number of new space group if you want to change the space group for the file of
structure factors. Program just changes space group name, group number and
cryst. symmetry operators, but not cell and data.
LIST < S | L >
Default: ~~
Sshort DOC-file
Llong DOC-file
DIFF < N | P | F | H >
Default:
Nuse unmodified structure factors
Puse modified stucture factors instead of Fobs for RF, as follows:
||Fobs|-|Fmod2|*(P2/100)|
Fuse modified stucture factors instead of Fobs for RF, as follows: vector
difference (Fobs - Fmod2*(P2/100))
Hfor heavy atom search
P2
Default: <0>
Percentage of model_2 in the structure.
NREF
Default: <10>
number of cycles of rigid body refinement for each TF solution.
see keyword:MODE
NREFP
Default: <0>
number of cycles of rigid body refinement before TF for each peak RF.
Default is without this refinement
STICK < N | Y >
Default:
Choose from symmetry-related models closest to which found before (this option
does not work with pseudo-translation possibility).
FILE_S
File with sequence for model correction by sequence alignment.
NMR < 0 | 1 | 2 | 3 >
Default: <0>
0use PDB file with NMR structures as single model
1use NMR possibility only for RF
2use NMR possibility for RF and TF. Best NMR model will be found and used
as solution.
3use NMR possibility for RF and TF. Averaged TF will be used. All NMR
models will be used as solution.
LOCK < Y | N >
Default:
Locked Cross Rotation function will be performed. Use also keywords: FILE_TSR
and NSRF
Keywords specific for multi-copy search
DYAD < N | Y | D >
Default:
Ymulti-copy search
Ddyad search
DIST
Three distances for dyad search.
DminDefault: radius of gyration. minimal distance between molecules
DmaxDefault: 1000Å. maximal distance between molecules
DparDefault: 1000Å. maximal shift along rotation axis
AXIS
Default: <0,0>
Chi
check only rotation by Chi (in degrees). 0 means to check all orientations.
Delta
delta for Chi (in degrees)
NSRF
Default: <0>
Number of peaks of Self-RF which will be used. 0 means not to use Self-RF. A
list of Self-RF peaks will be taken from file defined by keyword FILE_TSR which
must be prepared in advance (see Self Rotation Function).
NPT
This meaning only in conjuction with keyword DYAD: number of peaks in the STF
(Special Translation Function) to be checked through Translation Function
calculations, for inter-molecular vector search. If keyword DYAD is not given,
the standard meaning of keyword NPT is used.
NPTD
Number of peaks in TF to be checked through Correlation Coefficient
calculations, for dyad search.
NP2
Number of peaks in RF for second searching model to be checked for dyad search.
FILE_M2
file of second searching model
FILE_T2
file with list of peaks of RF for second searching model
ALL < N | Y >
Default:
if ALL = Y , program will use all Crystallographical Symmetry Operators
Keywords for Self Rotation Function
Without a file of the model, the program computes a Self Rotation Function.
CHI
Default: <60>
Angle chi of additional fourth section of RF(theta,phi,chi).
SCALE
Default: <6>
Maximum value of RF is SCALE * SIGMA(RF).
FILE_TSR
Default:
Input or output TAB_file with peaks of Self_RF.
Keywords for EM or electron density as model:
DSCALEM
Default: <1>
scale factor of correction of density cell
INVERM < N | Y >
Default:
If Y , inverted phases will be used
ROLIM
Default:
minimal value of density which will be used
DRAD
Default: <0>
radius of the model (in A). If parameter DRAD is defined program will use the
density only inside the sphere with radius = DRAD and with centre in vector
ORIGIN.
ORIGIN
Default: <0,0,0>
center of the model in the cell (in fract.units)
Keywords for EM or electron density instead of Fobs:
DSCALE
Default: <1>
scale factor of correction of density cell
INVER < N | Y >
Default:
If Y , inverted phases will be used
DLIM
Default:
minimal value of density which will be used
Keywords for pure Rigid Body Refinement:
DOM < N | Y | I | S >
Default:
NRB refinement as single body.
YMulti-domain refinement.
IGive only information about molecule-domain structure. Useful for RB
refinement with constraints.
SMulti-domain refinement with constraints.
MOLECULAR REPLACEMENT METHOD - THEORY
Molecular replacement method (MR)
There are two major steps in the Molecular replacement method: orientation and
translation search. They are performed by Rotation and Translation function.
Both of them are correlation functions (or overlapping functions) between
observed and calculated from model Patterson.
Rotation function (RF):
ROT(R) = I Pobs(r) * Pcalc(R,r) dr
radwhere
R
operator of rotation
I
rad
integral inside a sphere in the centre of patterson with radius=rad (i.e.
the cut-off radius)
Pobs
observed Patterson
Pcalc
calculated Patterson for rotated (R) model
Translation function (TF):
TR(s) = I Pobs(r) * Pcalc(s,r) dr =
cell
= Sum ( I Pobs(r) * Pcalc_ij(s,r) dr) = Sum TRij(s)
i#j i#jwhere
s
vector of translation
I
integral
i,j
cryst. symmetry operator numbers
Pcalc_ij(s,r)
calculated Patterson for model corresponding to ith operator and model
corresponding to jth operator
TRij(s)
translation function of Pattersons Pobs(r) and Pcalc_ij(s,r).
The Translation Function is the sum of translation functions for each pair of
different cryst. symmetry operators.
The best rotation function algorithm is the Crowther Fast Rotation Function
which we use here. It utilizes FFT. MOLREP can compute the Rotation Function for
three different orientations of the model and average them. That reduces the
noise of Rotation function.
Translation function algorithm was developed by the author and performs
calculations in the reciprocal space using FFT.
There are two major differences from other translation functions.
Instead of summation of the translation functions for two operators TRij, we
use their multiplication which makes the resulting map far more contrast-rich.
Finally we can multiply the translation function with the Packing Function to
remove peaks corresponding to incorrect solutions with bad packing.
Packing function (PF) is overlapping function:
P(s) = Sum ( I Ro_i(r) * Ro_j(r) dr )
i#j cellwhere Ro_i(r) is the electron density of the model which corresponds to the
ith cryst. symmetry operator.
The algorithm of calculation of the Packing Function is similar to the one
for the Translation Function and performed by the same program.
Finally the 'advanced' Translation function is:
TR(s) = [ M TRij(s) ] * P(s)
i#jwhere M means multiplication of different TRij.
Scaling by Patterson
For scaling we use a completely new strategy based on the Patterson origin peak
which is approximated by a Gaussian. This peak is computed for both the observed
and calculated amplitudes, and each case the B_overall is computed. The
difference
B_diff_overall = B_obs_overall - B_calc_overall
is then added to calculated B_overall so as to make the width of the calculated
Patterson origin peak equal to the observed peak. This method makes it possible
to have a good approximation for the scaling problem even if only low resolution
data is available where other methods do not work. Scaling by Patterson is also
useful for the Cross Rotation Function where we have different cells for the
model and the unknown structure.
Low resolution cut-off (Boff)
Low resolution cut-off introduces systematical errors in the electron density
especially near the surface of the model. This is known as the series
termination effect. Instead of using the usual low resolution cut-off, MOLREP
multiplies the modules of the structure factors by a special coefficient:
Fnew = Fold (1-exp(-Boff*s2)), where Boff= 4resmin2Boff is called the "soft low resolution cut-off", which allows removal of
structure factors in this resolution range without inroducing the series
termination effect.
The use of a priori knowledge of similarity and completeness of the model
For low similarity the high resolution reflections are weighted down. For this,
MOLREP uses an additional overall factor Badd:
Fnew = Fold exp(-Badd*s2)Value of similarity 'SIM' can be: from 0.1 to 1.0. It corresponds to Badd: from
(B_limit-Boverall) to -Boverall, where B_limit + 80.
SIM=1 means normalized F will be used.
For low completeness, e.g. when there are several molecules in the a.u., the
contribution of low resolution reflections is weighted down. To manage the
completeness of the model, MOLREP uses a low resolution cut-off (Boff).
Completeness of model 'COMPL' can be : from 0.2 to 1.0. It corresponds to Boff:
from 400 to 1600.
Functions of electron density searching (SM)
We suggest a new approach to divide a phased six-dimensional search into three
steps:
A spherically averaged translation function is used to locate the position of
a molcule or its fragment. It compares locally spherically averaged
experimental electron density with that calculated from the model and
tabulates highly probable positions accordingly.
Then for each position a local phased rotation function is used to find the
orientation of the molecule.
The third step is the phased translation function, used to check and refine
the found position.
Spherically averaged phased translation function (SAPTF)
SAPTF gives the expected position of a model in an electron density map by the
comparison of spherically averaged density of the model with locally spherically
averaged observed density.
SAPTF(s) = I Robs(r,s) * Rcalc(r) dr
rad(s)where
I
rad(s)
integral inside a sphere centred in point s of electron density with
radius=rad (i.e. the cut-off radius)
Robs
spherically averaged around point s observed electron density
Rcalc
spherically averaged around origin of coordinate system calculated electron
density for model
Phased Rotation function (PRF)
PRF gives the orientation of model placed in some point of electron density.
PROT(O) = I Robs(r) * Rcalc(O,r) dr
rad(s)where
O
operator of rotation
I
rad(s)
integral inside a sphere centred in point s of electron density with
radius=rad
Robs
observed electron density
Rcalc
calculated electron density for rotated (O) model
Phased Translation function (PTF)
Translation search in electron density map.
PTR(s) = I Robs(r) * Rcalc(s,r) dr
cellwhere
s
vector of translation
I
integral
Robs
observed electron density
Rcalc(s,r)
calculated electron density for model placed in the vector s
Fitting two models (FM)
Fitting through electron density. Second model (MODEL_2) is the target model
which converted to electron density. To search the best overlapping of electron
densities of models there are two algorithms:
Rotation Function (Patterson) and Phased Translation Function (electron
density).
All functions for electron density. Spherically Averaged Phased Translation
Function gives expected position for model. Phased Rotation Function for
expected position gives orientation. Phased Translation Function checks and
refines the translation vector.
Special Translation Function (STF) for dyad search
Multi-copy search
Search two copies of a model simultaneously. There are three stages to this:
Rotation function. The program checks all pairs of first NP peaks of Rotation
Function (RF). For each pair the program uses the first rotation to prepare
model-1. Model-2 will be prepared by using the second rotation and one
rotation from the crystallographical symmetry operatators.
Next, for the current pair (model-1 and model-2): MOLREP computes the Special
Translation Function (STF) to find the inter-molecular vector of this dyad.
For NPT peaks of the previous Special Translation Function (STF) (i.e. for NPT
inter-molecular vectors) the program computes a standard Translation Function
(TF) using the current dyad as model and calculates a Correlation Coefficient
for first NPTD peaks of TF.
Special Translation Function (STF)
Imagine two models in the asymm. part of the unit cell:
F1(h)
structure factor of model_1 with the centre of gravity in the origin of the
coord. system
F2(h)
structure factor of model_2
Let
S1
vector in unit cell from the origin of the coord. system to the centre of
gravity of model_1
S2
vector for model_2
When F(h) is the total structure factor (for the whole crystal structure):
F(h) = F1(h)exp(-2pihS1) + F2(h)exp(-2pihS2)Then the Patterson is:
P(h) = F(h)*F'(h)
= F1(h)*F1'(h)
+ F1'(h)*F2(h)*exp(-2pih(S2-S1))
+ F2'(h)*F2(h)
+ F1(h)*F2'(h)*exp(-2pih(S1-S2))
= P0(0) + P1(S2-S1) + P1(S1-S2)The Special Translation Function is a Phased TF with a Patterson function as
electron density and P1 = F1'(h)*F2(h) as structure factors of the model.
Solution of this function is the dyad vector S1-S2.
Anisotropic correction and scaling
Aniso correction:
For Structure Factors we can estimate:
1. isotropic B_overal:
F(s) ~ Scale_overall * exp (-B_overall*s^2)
2. anisotropic B_overall (tensor) :
F(s) ~ Scale_overall * exp(-(B11a*a*hh +2B12a*b*hk+..)
Aniso correction means to make data isotropic with B_overall:
F_new(s) = F_old(s) * exp(+(B11a*a*hh +2B12a*b*hk+..) * exp(-B_overall*s^2)
Aniso scaling:
Fnew = Scale*Fold*exp(-(B11a*a*hh +2B12a*b*hk+..)
Scale ans aniso B are taken by mimimization: sum(!Fobs-Fnew!)
COMMAND FILE EXAMPLES
example of Cross Rotation and Translation functions:
# --------------------------------
molrep HKLIN test.mtz MODEL 2sar.pdb << eor
# --------------------------------
#
LABIN F=F SIGF=SIGF
NP 8
RAD 27
ANISO C
sim .1
compl .5
eor
example of Self Rotation function:
# --------------------------------
molrep HKLIN test.mtz << eor
# --------------------------------
#
LABIN F=F SIGF=SIGF
#
RAD 27
END
eor
example using phases
For searching in the electron density map for some model (standard Rotation
Function will be used):
# --------------------------------
molrep HKLIN test.mtz MODEL mod.pdb << eor
# --------------------------------
#
LABIN F=F SIGF=SIGF PH=PH_FO FOM=FOM
#
NP 8
END
eor
example of fitting two models:
# --------------------------------
molrep MODEL mod.pdb MODEL2 mod2.pdb << eor
# --------------------------------
#
PRF Y
eor
example of dyad search:
# --------------------------------
molrep HKLIN test.mtz MODEL mod.pdb << eor
# --------------------------------
#
LABIN F=F SIGF=SIGF
#
dyad y
axis 0,10
dist 0,300,300
NPT 3
NPTD 3
eor
example of dimer search:
# --------------------------------
molrep HKLIN test.mtz MODEL mod.pdb << eor
# --------------------------------
#
LABIN F=F SIGF=SIGF
#
dyad y
axis 180,10
dist 0,300,1
NPT 3
NPTD 3
eor
example dimer search for Self-RF orientations:
# --------------------------------
molrep HKLIN test.mtz MODEL mod.pdb << eor
# --------------------------------
#
LABIN F=F SIGF=SIGF
#
dyad y
axis 180,10
dist 0,300,1
NSRF 20
NPT 3
NPTD 3
FILE_TSR srf.tab
eor
example of using file of sequence
# --------------------------------
molrep HKLIN test.mtz MODEL mod.pdb << eor
# --------------------------------
#
LABIN F=F SIGF=SIGF
#
NP 8
NMON 2
FILE_S new.seq
sim .1
compl .5
eor
Convention for rotation
Rotation by Euleran angles Alpha, Beta, Gamma:
euleran angles : 1. A( Z ) - alpha around axis Z
2. B( Y') - beta around new axis Y
3. G( Z') - gamma around new axis Z
Rotation by Polar angles Theta, Phi, Chi:
polar coordinates Theta, Phi of rotate axis:
Theta - angle between rotate axis and Z
Phi - angle in plan XY between X and projection rotate axis
Chi - rotation angle arount rotate axis
Convention for Orthonormal coordinate system
Orthonormal axes are defined to have:
A parallel to X , Cstar parallel to Z
MEMORY CONTROL PARAMETERS
In main_molrep_mtz.f:
CC --- MEMORY - common memory for maps and coordinates
PARAMETER ( MEMORY =4000000 )
CC --- NCRDMAX - maximal number of coordinates
PARAMETER ( NCRDMAX = 100000 )
CC --- IPRSYM - maximal number of symmetry operators
PARAMETER ( IPRSYM=96 )
INTEGER*2 ISYM(5,3,IPRSYM)
PARAMETER ( MEM = MEMORY/2 )
REAL*8 POOL(MEM)
C ----
If program stops with message:
ERROR: not memory enough ...change parameter MEMORY in main_molrep_mtz.f
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This page was last updated on May 09, 2005
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