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]
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.
Without this file the program computes a Self Rotation Function and plots RF(theta,phi,chi) for
chi = 180, 90, 120, 60You can change the fourth value of chi (60) by keyword CHI
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.
"Sol_ 23 10.0 22.2 40.0"
If you like to use Eiler angles use "Sol_A" instead "Sol_""Sol_ 23 10.0 22.2 40.0 .564 .443 .032"
But program will use only the shift (sx,sy,sz)."Sol_ 23 10.0 22.2 40.0 .564 .443 .032"
also (if you used keyword FILE_S):
+-- 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
The program performs molecular replacement in two steps:
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
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:
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:
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
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.:
But program will use only the shift (sx,sy,sz)."Sol_ 23 10.0 22.2 40.0 .564 .443 .032"
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
The idea is to fit the electron densities instead of the atomic models, trying to find the best overlap. Advantages are:
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.
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
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.
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
You can improve your model beforehand by using keyword SURF.
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.
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
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 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,
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
Use keywords:
FUN = D, MODEL_2,
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.
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.
Success of the molecular replacement method depends on:
Things to look out for:
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
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.
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).
The available keywords are:
General keywords
Common:
DOC, LABIN, FILE_T, FUN, NMON, NP, NPT, RAD PATH_SCRAnd for structure factors control:
COMPL, RESMAX, SIMAnd for model control:
SURFAnd for multi-copy search:
DYAD, FILE_M2, FILE_T2, NP2, NPTD, NSRFAnd for search in ED:
PRF, INVERAnd for fitting two models:
PRFAnd for EM or electron density model:
DSCALEM, INVERM, ROLIM, DRAD, ORIGINAnd for EM or electron density instead of Fobs:
DSCALE, INVER, DLIMKeywords for special cases
Common:
ANISO, BADD, LIST, LMAX, LMIN, MODE, PACK, RES_R, RES_TAnd for standard MR:
DIFF, FILE_S, NMR, NOSG, P2, PST, STICK, VPST, LOCK, NREF, NREFPAnd for Self RF:
CHI, PST, SCALE, FILE_TSRAnd for multi-copy search:
AXIS, DIFF, DIST, P2, ALL, STICKAnd for search in ED:
DIFF, P2, NPTDAnd for fitting two models:
NPTDAnd for Pure Rigid Body Refinement:
DOM
Specify input column lables.
The program labels defined are: F, SIGF, F(-), SIGF(-), I,SIGI, I(-), SIGI(-), PHIC, FOM
| F | label of F or F(+) |
|---|---|
| SIGF | label of sigma F or sigma F(+) |
| F(-) | label of F(-) |
| SIGF(-) | label of sigma F(-) |
| I | Structure Intensity of hkl |
| SIGI | Standard deviation of the above |
| I(-) | Structure Intensity of -h -k -l |
| SIGI(-) | Standard deviation of the above |
| PH | label of phases |
| FOM | label of figure of merit |
Default: <N>
use the additional file with the protocol of the running of the program: DOC-file molrep.doc
| N | do not produce DOC-file |
|---|---|
| Y | produce DOC-file with new contents |
| A | keep 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.
Default: <10>
<np> 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.
Default: <20>
<npt> 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.
Default: <1>
<nmon> is the number of monomers. The program will try to create a full model, which will consist of NMON initial models plus model_2.
Default: automatic choice
<compl> 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.
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.
The use of Boff and Badd means to change Fobs and Fmodel:
|F|_new = |F|_input *exp(-Badd*s2)*(1-exp(-Boff*s2)
Default: <A>
| R | calculate only Rotation Function |
|---|---|
| T | calculate only Translation Function, reading list of peaks of RF from file (molrep_rf.tab) or from TAB_file |
| A | calculate both: RF and TF |
| S | rotate and position the model and compute R-factor and Correlation Coefficient |
| B | pure Rigid Body refinement |
| D | find HA positions by MR solution |
Default: <molrep_rf.tab>
Input or output TAB_file (see also molrep_rf.tab)
Default: <Y>
Perform model correction.
| N | do not perform any model correction.For FUN=S (just_rotate_and_position) program changes N to O | O | only shift to the origin | A | make 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 | Y | remove 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 | 2 | set all B = 20 and shift to the origin |
|---|
Default: automatically calculated from the model, unless:
Cut-off radius for Patterson search or for electron density search.
Default: <3>
High resolution limit.
Default: <N>
How to deal with pseudo-translation.
| N | ignore pseudo-translation altogether |
|---|---|
| C | check 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. |
| Y | use 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. |
Default: automatically from Patterson
Pseudo-translation vector (in fractional units), used when PST = Y.
Default: <F>
| F | standard rotation and translation functions are used without rigid body refinement |
|---|---|
| S | advanced rotation and translation functions and rigid body refinement are used |
| M | standard rotation and translation functions are used. Rigid body refinement is possible. Rather slow then MODE=F, but correlation coefficient is calculated more correctly. |
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.
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.
Default: <0>
|F|_new = |F|_input *exp(-Badd*s2)*(1-exp(-Boff*s2)
Default: <N>
| N | do not use anisotropic correction and/or scaling |
|---|---|
| Y | use anisotropic correction and scaling |
| C | use anisotropic correction of Fobs for RF only |
| S | use anisotropic scaling for TF only |
| K | use scaling without B-factor |
Default: <Y>
| Y | use Packing Function with Translation Function |
|---|---|
| N | do not use Packing Function with Translation Function |
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.
Default: automatic choice
Maximum L-index of spherical coefficients. Possible values are 2,4,6,8,...,58,60.
Default: <N>
| N | standard RF and Phased Translation Function is calculated |
|---|---|
| Y | SAPTF (Spherically averaged phased translation function), Phased Rotation Function (PRF) and Phased Translation Function will be used. |
| S | SAPTF (Spherically averaged phased translation function), Usual Rotation Function (RF) for modified map and Phased Translation Function will be used. |
| P | Search 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)"
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.
Default: <S>
| S | short DOC-file |
|---|---|
| L | long DOC-file |
Default: <N>
| N | use unmodified structure factors |
|---|---|
| P | use modified stucture factors instead of Fobs for RF, as follows: ||Fobs|-|Fmod2|*(P2/100)| |
| F | use modified stucture factors instead of Fobs for RF, as follows: vector difference (Fobs - Fmod2*(P2/100)) |
| H | for heavy atom search |
Default: <0>
Percentage of model_2 in the structure.
Default: <10>
number of cycles of rigid body refinement for each TF solution.
see keyword:MODE
Default: <0>
number of cycles of rigid body refinement before TF for each peak RF.
Default is without this refinement
Default: <N>
Choose from symmetry-related models closest to which found before (this option does not work with pseudo-translation possibility).
File with sequence for model correction by sequence alignment.
Default: <0>
| 0 | use PDB file with NMR structures as single model |
|---|---|
| 1 | use NMR possibility only for RF |
| 2 | use NMR possibility for RF and TF. Best NMR model will be found and used as solution. |
| 3 | use NMR possibility for RF and TF. Averaged TF will be used. All NMR models will be used as solution. |
Default: <N>
Locked Cross Rotation function will be performed. Use also keywords: FILE_TSR and NSRF
Default: <N>
| Y | multi-copy search |
|---|---|
| D | dyad search |
Three distances for dyad search.
| Dmin | Default: radius of gyration. minimal distance between molecules |
|---|---|
| Dmax | Default: 1000Å. maximal distance between molecules |
| Dpar | Default: 1000Å. maximal shift along rotation axis |
Default: <0,0>
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).
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.
Number of peaks in TF to be checked through Correlation Coefficient calculations, for dyad search.
Number of peaks in RF for second searching model to be checked for dyad search.
file of second searching model
file with list of peaks of RF for second searching model
Default: <N>
if ALL = Y , program will use all Crystallographical Symmetry Operators
Without a file of the model, the program computes a Self Rotation Function.
Default: <60>
Angle chi of additional fourth section of RF(theta,phi,chi).
Default: <6>
Maximum value of RF is SCALE * SIGMA(RF).
Default: <molrep_srf.tab>
Input or output TAB_file with peaks of Self_RF.
Default: <1>
scale factor of correction of density cell
Default: <N>
If Y , inverted phases will be used
Default: <not used>
minimal value of density which will be used
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.
Default: <0,0,0>
center of the model in the cell (in fract.units)
Default: <1>
scale factor of correction of density cell
Default: <N>
If Y , inverted phases will be used
Default: <not used>
minimal value of density which will be used
Default: <N>
| N | RB refinement as single body. |
|---|---|
| Y | Multi-domain refinement. |
| I | Give only information about molecule-domain structure. Useful for RB refinement with constraints. |
| S | Multi-domain refinement with constraints. |
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.
ROT(R) = I Pobs(r) * Pcalc(R,r) dr
rad
where
- 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
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#j
where
- 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.
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.
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 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= 4resmin2
Boff is called the "soft low resolution cut-off", which allows removal of structure factors in this resolution range without inroducing the series termination effect.
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.
We suggest a new approach to divide a phased six-dimensional search into three steps:
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
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
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 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:
Search two copies of a model simultaneously. There are three stages to this:
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.
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!)
# -------------------------------- molrep HKLIN test.mtz MODEL 2sar.pdb << eor # -------------------------------- # LABIN F=F SIGF=SIGF NP 8 RAD 27 ANISO C sim .1 compl .5 eor
# -------------------------------- molrep HKLIN test.mtz << eor # -------------------------------- # LABIN F=F SIGF=SIGF # RAD 27 END eor
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
# -------------------------------- molrep MODEL mod.pdb MODEL2 mod2.pdb << eor # -------------------------------- # PRF Y eor
# -------------------------------- 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
# -------------------------------- 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
# -------------------------------- 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
# -------------------------------- 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
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
Orthonormal axes are defined to have:
A parallel to X , Cstar parallel to Z
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