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 117121. Alexei Vagin and Alexei Teplyakov. An approach to multicopy search in molecular replacement., Acta Cryst.D,(2000) 56, pp 16221624 A.A.Vagin and M.N.Isupov Spherically averaged phased translation function and its application to the search for molecules and fragments in electrondensity maps Acta Cryst.D,(2001) 57, pp 14511456 main: A.Vagin,A.Teplyakov, MOLREP: an automated program for molecular replacement., J. Appl. Cryst. (1997) 30, 10221025.
Copy file molrep.tar.gz
and uncompress it (`gunzip molrep.tar.gz')
After untaring `molrep.tar' (command: tar xvf molrep.tar) you will get a molrep directory, with src, doc, data, molrep_check and bin subdirectories and README file. To build the executable, go to src.
Also you can download binaries (executable files):
molrep_linux.gz
molrep_macintel.gz
Tutorials:
also you can use Testing_program_MOLREP as tutorial
You can use this version as previous one: 1. by command (batch) file 2. interactively 3. by ccp4i New style to use: You can use program by command string with options: molrep f file_sf_or_map m model_crd_or_map mx fixed model m2 model_2 po path_out ps path_scrath s file_sequence s2 file_seq_for_m2 k file_keywords doc y_or_a_or_n h i r h = only keyword and mtz label information, clean i = interactive mode r = rest some special files file_keywords = simple text file with keywords (one line  one keyword) Examples: Without any keywords: Usual MR: RF + TF molrep f file.mtz m model.pdb Usual MR with fixed model molrep f file.mtz m model.pdb mx mfix.pdb Usual MR with sequence and redirect output and scratch files molrep f file.mtz m model.pdb s file_seq po out/ ps scr/ Self rotation funtion molrep f file.mtz multicopy search, one model (DYAD M) molrep f file.mtz m model.pdb m2 model.pdb multicopy search, two different models (DYAD M) molrep f file.mtz m model1.pdb m2 model2.pdb Fitting two atomic models molrep m model1.pdb mx model2.pdb Rigid body refinement molrep f file.mtz mx model.pdb Get information about keywords and mtz labels, and clean molrep h f file.mtz If you like to play with keywords: Using keywords from file molrep f fobs.pdb m model.pdb k file_keywords Using keywords interactivly molrep f file.mtz m model.pdb i "CR" sim .4 "CR" sg all "CR" "CR" Script example:  molrep f fobs.mtz m model.pdb i <<stop fun t file_t tab stick n stop 
Use "molrep h" to get short manual of MOLREP.
You can stop program safely if you create in current directory or in PATH_OUT (if option po is used) file:
molrep_stop_signal.xml
(contents does not matter)
new value M means "multimonomer search", new algorithm of Multicopy search . Instead to search two copies and then next one program constructs maximal possible complexes of monomers (3mres,4mers,5mers,...) and checks its by TF. 
N means do not stop if contrast is good and do not assess solution.
Scoring system is working well if expected number of models and
proper symmetry of model are correct.Proper symmetry of model
program defines by model Self Rotation Funtion when Cross Rotation
function is computed. If you like or if you use keyword FUN = T you can define Proper symmetry of model by keyword NCSM. 

C use Correlation Coeffitient instead of score and do not stop.
score is product Correlation Coeffitient, value of Packing function and maximal value of Packing index. contrast means: >3.0  definitly solution <3.0 and > 2.0  solution <2.0 and > 1.5  maybe solution <1.5 and > 1.3  maybe not solution, but program accepts it <1.3  probably not solution. 
number of subunits in the model (only for scoring) 
new value A means to check all pseudotranslation vectors automatically (default now). 
new value M means to remove fixed model from map (Fobs,PHobs) by mask for RF or PRF. 
space group name. You can use this keyword instead NOSG ALL means to check all possible space groups automatically. 
soft resolution cut_off, use it instead COMPL 
D  default: to use identity as SIM and to use corrected model only if identity > 20% 

N  means to use identity as SIM only (without model correction) 
Y  means to use identity as SIM and to use corrected model 
as Y but new B only for Packing function, not change original B 
Y is default. SURF for fixed model (no shift to origin) 
A  after RF program computes Self_RF and use from RF only related peaks for TF. 

You can find some examples in Input file examples.
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 keywords NOSG or SG .
"Sol_ 23 10.0 22.2 40.0"
"Sol_ 23 10.0 22.2 40.0 .564 .443 .032"
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"
Some output files will not be deleted if option "r" in command string was used. They have the internal format of the BLANC program suite and can be used by programs of this suite.
also (if you started from MTZ file):
also (if you used keyword FILE_S):
See also How to redirect output and scratch files
+ 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 ) ! ! ! + identical models ! ! ! +Multimonomer+ ! ! search ! ! ! (DYAD=M) + complex with pairs of ! ! different models ! ! ! ! + two identical models ! ! ! + Multicopy search + Dyad search + ! for MR ! (DYAD=D) ! ! ! + two different ! ! models ! ! MOLREP + + Multycopy 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_T2) ! ! ! + 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 (phased or unphased, FUN=B, model_2) where: FUN, DYAD, PRF, LOCK, DIFF  keyword 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 socalled cutoff 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 (keyword RAD).
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 (MODEL_2), the use of modified stucture factors instead of Fobs for RF (keywords DIFF,P2) may make RF clearer. The modified stucture factor is:
sqrt(IobsImod2*(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 (NP) 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 (ANISO). The Translation function can take into account the second fixed model (MODEL_2) 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 symmetryrelated models closest to which was found before is useful (keyword STICK).
The program can detect and use pseudotranslation vectors. In this case the pseudotranslation 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 symmetryrelated or different models (keyword PACK).
Be careful, with keyword SURF='Y' program use to calculate Packing Function only atoms which lying inside of molecule.So, for nonglobular model (for example, only CA atoms) you cannot use keyword SURF='Y' with PACK='Y'.
Use keywords:
DIFF, FUN, MODEL_2, NMON, NP, NPT, P2, PACK, PST, RAD, RESMAX, RESMIN, SIM, STICK, SURF, VPST, FILE_T, FILE_TSRF, NSRF
If you define only a file of structure factors (Fobs), the program will compute a Self Rotation function with default value of cutoff radius. Use keyword RAD if you want another value. Other useful keywords: RESMAX, RESMIN, SIM.
Resulting output:
In some cases it is difficult to solve an Xray 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 sixdimensional search. The program divides the sixdimensional 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. In EM case map will be converted into !F! and phases.
For input map use keywords:
DSCALE, INVER, DLIM
 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
SFCHECK can convert input map to scaled and/or inverted map.
If you structure contains several molecules which forms some point group you can use this NCS. Program will generate complete model and use it for stage PTF. Also result (molrep.pdb) will be complete model.
First of all you must define parameters of NCS in PDB file or using keywords NCS, ANGLES, CENTRE. See How to define NCS
Other useful keywords:
NMON, NP, NPT, RAD, RESMAX, RESMIN, SIM, SURF, INVER, NCS, ANGLES, CENTRE
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_T2 , 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:
NMON, NP, NPT, RESMAX, RESMIN, 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 (Fobs), the program will fit the search model (keyword FILE_M) to the second model (keyword MODEL_2). 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':
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:
NP, NPT, RAD, RESMAX, RESMIN, SIM, SURF
The result is file molrep.crd (or 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 (keyword FILE_M), a file of structure factors (keyword FILE_F) 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 Rfactor and a Correlation Coefficient.
If you like to use Eiler angles use "Sol_A" instead "Sol_" see molrep_rf.tab
If you like to rotate around some atom, you have to shift coordinate system origin to this atom by hand and use keyword SURF = N.
Other useful keywords:
RESMAX, RESMIN, SIM
There are three modes: "dyad_search", "Multicopy search"and "Multimonomer 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 multicopy 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 model1
 R2
 peak number of rotation for model2
 Rs
 CS operator number which applyed before rotation for model2
 Rslf
 peak number of self rotation function
 STF
 peak number of special translation function
 TF
 peak number of translation function
 Shift_1
 position of model1
 PFmax PFmin
 min, max values of Packing function
 Rfac Corr
 Rfactor and Correlation Coefficient
 Rot1>2
 polar angles of rotation from model1 to model2.
 Dyad_vector
 vector (in fractional) from model1 to model2.
 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.
Also 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 SelfRF, you can try to find a dyad which has the rotation between monomers corresponding to the rotation of the SelfRF (use keywords NSRF,FILE_TSRF).
Model2 can be different from model1. Use keywords FILE_M2 to define file of searching model2, 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.
Multicopy 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.
Multimonomer search  construct complexes of monomers and check. (keyword DYAD=M).
Instead to search two copies and then next one program constructs maximal possible complexes of monomers (3mres,4mers,5mers,...) and checks its by TF. This algorithm is better and faster then DYAD=D or DYAD=Y. But also it takes a time (about 30min,1h,2h ...). It depends on resolution, size of cell, space group.
Use keywords:
DYAD, DIST, NP, NSRF, NPT, NPTD, NP2, AXIS, FILE_M2, FILE_T2, FILE_T, FILE_TSRF, NMON, ALL, PACK
For DYAD M:
DYAD, NP, NPTD, NP2, FILE_M2, FILE_T2, FILE_T, NMON, ALL, PACK NML
and also:
SIM, RESMAX, RESMIN, SURF, STICK
You can improve your model beforehand by using keyword SURF.
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 
C  as Y but new B only for Packing function (not change original B) and shift to the origin 
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:
!> title !# sequence !SVIGSDDRTRVTNTTAYPYRAIVHISSSIGSCTGWMIGPKTVATAGHCIY !# this is comment ! DTSSGSFAGTATVSP 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. Without an Fobs file, the program only performs model correction.
You can use PDB file with NMR models or pseudoNMR 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, ORIGINSearch model in electron density map will be performed as usual.
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_TSRF,
You can use Rigid Body Refinement in Patterson or Real space (keyword FUN = 'B'). This possibility is useful in the last stage of MR. For example after fitting the model into EM map. You must define Fobs or Fobs and phases (or Map). Also use keyword MODEL_2 for model to refine. If you define the phases or use the map program will produce real space refinement (more correctly, in reciprocal space using phase information).
If keyword DOM = 'N' (default) program refines MODEL_2 as single molecule.
If keyword DOM = 'Y' program performs multidomain refinement. For this you must put into PDB file additional lines before each domain. Additional line contains word '#DOMAIN' and domain number (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 ... ...
If you structure contains several molecules which forms some point group you can use this NCS as constraints. First of all you must define NCS parameters in PDB file or using keywords: NCS,ANGLES, CENTRE. See How to define NCS
If you have some trouble with NCS parameters (values: theta,phi,chi,cx,cy,cz) use keyword DOM = 'I' and you can find these actual values in output PDB file: molrep.pdb. Alternative way to create initial PDB file with complete model is to describe only first (reference) molecule and use keyword DOM = 'C'. Complete model you can find these in output PDB file:molrep.pdb. Finally use keyword DOM = 'S' for refinement with constraints.
Use keywords:
FUN = B, DOM, SIM, RESMAX, RESMIN, NREF, NCS, ANGLES, CENTRE
To define derivative use corresponding label for MTZ file or derivative file (FILE_DER).
Use keywords:
FUN = D, MODEL_2 (as MR solution)
To define derivative use corresponding label for MTZ file or derivative file (FILE_DER).
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.
(you can use Testing_program_MOLREP as tutorial)
A simple way to use MOLREP is to define files for Fobs and the model 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:
You can use MOLREP by dialogue or by command (batch) file. Modern computing technology allows the carrying out of most of the calculations for small and medium sized proteins in real time, therefore, dialogue is a preferable way of running MOLREP. However, the program automatically produces a batch command file during dialogue. This feature might be useful for repeated calculations.
MOLREP can detect pseudotranslation, and define a pseudotranslation vector.
If keyword PST = Y, the program applies pseudotranslation with a pseudotranslation 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. Pseudotranslation 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 pseudotranslation.
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 or DYAD = M)
2. Solve one domain, refine it and use the solution as fixed model to solve another domain.
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).
It is easy to use MOLREP interactively, but can be used in batch. The available keywords are:
General keywords
Common:
FILE_T, FUN, NMON, NP, NPT, RAD PATH_SCRAnd for structure factors control:
RESMAX, RESMIN, SIMAnd for model control:
MODEL_2, SURFAnd for multicopy search:
DYAD, FILE_M2, FILE_T2, NP2, NPTD, NSRFAnd for search in ED:
PHASE, 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, PACK,And for standard MR:
DIFF, FILE_S, NMR, NOSG, P2, PST, STICK, VPST, LOCK,And for Self RF:
CHI, PST, SCALE, FILE_TSRFAnd for multicopy search:
AXIS, DIFF, DIST, P2, ALL, STICKAnd for search in ED:
DIFF, P2, NPTDAnd for fitting two models:
NPTDAnd for search in ED:
NCS, ANGLES, CENTREAnd for Pure Rigid Body Refinement:
DOM, NCS, ANGLES, CENTRE
Default: <auto>
<np> is the number of peaks from the rotation function to be used (maximum: 200).
Default: <15>
<npt> is the number of peaks from the translation function to be used (maximum: 50).
Default: <auto>
<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: <auto>
soft resolution cut_off: Boff =2*RES_min^2
Default: automatic choice
COMPL = V_model/(V_cell/Nsym), RESMIN ~ Rad_model. It corresponds to Boff:
Default: 0.35
Similarity of the model: from 0.1 to 1.0. It corresponds to Badd. SIM=1 means normalized F will be used. SIM=1 means do not use SIM (i.e. BADD=0) 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*s^{2})*(1exp(Boff*s^{2})
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 Rfactor 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: no model_2
Input file with the second (fixed) model in correct position and orientation, in PDB or BLANC format. This model will be fixed during the search. When fitting two models to each other, the second model is the target model.
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 
C  as Y but new B only for Packing function (not change original B) and shift to the origin 
Default: automatically calculated from the model, unless:
Cutoff radius for Patterson search or for electron density search.
Default: <auto>
High resolution limit.
Default: <not used>
Path to directory for scratch files. For example: /y/people/alexei/
Default: <N>
How to deal with pseudotranslation.
N  ignore pseudotranslation altogether 

C  check only, but do not use pseudotranslation 
Y  use pseudotranslation. 
Default: automatically from Patterson
Pseudotranslation vector (in fractional units), used when PST = Y.
Default: <0>
F_new = F_input *exp(Badd*s^{2})*(1exp(Boff*s^{2})
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 Bfactor 
Default: <Y>
Y  use Packing Function with Translation Function 

N  do not use Packing Function with Translation Function 
Default: <4>
Minimum Lindex 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 Lindex of spherical coefficients. Possible values are 2,4,6,8,...,98,100.
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_T2. 
Program will use the phases of BLANC (by keyword PHASE) or 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: none
BLANC file of phases. If input Fobs file is CIF use 'PHASE +'. It means to use the phases from CIFile.
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: < >
New space group name. "ALL" means to check all possible SG.
Default: <N>
N  use unmodified structure factors 

P  use modified stucture factors instead of Fobs for RF, as follows: sqrt(IobsImod2*(P2/100)) 
F  use modified stucture factors instead of Fobs for RF, as follows: vector difference (Fobs  Fmod2*(P2/100)) 
M  remove fixed model from diff. fourie by mask (model_2). 
H  for heavy atom search 
Default: <0>
Percentage of model_2 in the structure.
Default: <5>
number of cycles of rigid body refinement.
Default: <Y>
Choose from symmetryrelated models closest to which found before (this option does not work with pseudotranslation 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_TSRF and NSRF
Without FILE_TSRF program computes Self_RF and uses NSRF peaks from it.
Default: <N>
A means after RF to compute Self_RF and use from RF only related peaks for TF.
If you like you can use keyword: NSRF
Default: <Y>
N  do not stop if contrast is good 

C  Corr.Coef. instead Score and do not stop 
Default: <N>
Y  multicopy search 

D  dyad search 
M  multimonomer 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 SelfRF which will be used. 0 means not to use SelfRF. A list of SelfRF peaks will be taken from file defined by keyword FILE_TSRF which must be prepared in advance (see Self Rotation Function).
Number of peaks in the STF (Special Translation Function) to be used.
Number of peaks in TF to be used.
Number of peaks in RF for second searching model to be used 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
number of Nmers to check (DYAD = "M").
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  Multidomain refinement. 
I  Give only information about moleculedomain structure. Useful for RB refinement with constraints. 
S  Multidomain refinement with constraints. 
C  only create complete model using NCS parameters. See How to define NCS 
Default: <0>
NCS identifier or = "1" which means to use NCS parameters from file.
Default: <0,0,0>
Polar angles of NCS which define the standard system orientation in the cell.
Default: <0,0,0>
position of the NCS centre in the cell (in fract.units)
Input file of derivative or use labels for MTZ file.
The best and easiest way to prepare a command file is to run MOLREP once by dialogue. The program creates a command (batch) file (molrep.btc) automatically.
See some command (batch) file examples.
The following keywords are necessary only for MTZ files.
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 Intensity of hkl 
SIGI  Standard deviation of the above 
I()  label of Intensity of h k l 
SIGI()  Standard deviation of the above 
PH  Label of phases 
FOM  Label of figure of merit 
FD  Label of Fderivative 
SIGFD  Label of sigma Fderivative 
DP  Label of !F(+)!!F()! 
SIGDP  Label of DP 
(also you can use this as tutorial)
In directory "../molrep/molrep_check/" there are two files:
In directory "../molrep/molrep_check/data/" there are several files for Xray test:
In directory "../molrep/molrep_check/em/" there are several files for EM test:
See "../molrep/molrep_check/readme"
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 P_{obs}(r) * P_{calc}(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 cutoff radius)
 P_{obs}
 observed Patterson
 P_{calc}
 calculated Patterson for rotated (R) model
TR(s) = I P_{obs}(r) * P_{calc}(s,r) dr = cell = Sum ( I P_{obs}(r) * P_{calc_ij}(s,r) dr) = Sum TR_{ij}(s) i#j i#j
where
 s
 vector of translation
 I
 integral
 i,j
 cryst. symmetry operator numbers
 P_{calc_ij}(s,r)
 calculated Patterson for model corresponding to ith operator and model corresponding to jth operator
 TR_{ij}(s)
 translation function of Pattersons P_{obs}(r) and P_{calc_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):The overlap for the model in the position s
O(s) = Sum (I Ro_i(r,s) * Ro_j(r,s) dr), where i#j i,jwhere Ro_i(r,s) is the electron density of the model which corresponds to the ith cryst. symmetry operator.
Packing function:
P(s) = 1  scale * O(s)scale is chosen to make overlap of one copy with itself equal one, i.e. to make
I Ro_i(r,s) * Ro_i(r,s) dr = 1Finally we have P(s) = 1 for no overlap. Negative values are converted to 0.
If we have a fixed model
O(s) = Sum (I Ro_i(r,s) * Ro_j(r,s) dr) + Sum (I Ro_fixed(r) * Ro_i(r,s) dr)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 TR_{ij}(s) ] * P(s) i#jwhere M means multiplication of different TR_{ij}.
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 cutoff 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 cutoff, MOLREP multiplies the modules of the structure factors by a special coefficient:
Fnew = Fold (1exp(Boff*s^{2})), where Boff= 2resmin^{2}
Boff is called the "soft low resolution cutoff", 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*s^{2})
Value of similarity 'SIM' can be: from 0.1 to 1.0. It corresponds to Badd: from (B_limitBoverall) 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 cutoff (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 sixdimensional 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 R_{obs}(r,s) * R_{calc}(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 cutoff radius)
 R_{obs}
 spherically averaged around point s observed electron density
 R_{calc}
 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 R_{obs}(r) * R_{calc}(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
 R_{obs}
 observed electron density
 R_{calc}
 calculated electron density for rotated (O) model
Translation search in electron density map.
PTR(s) = I R_{obs}(r) * R_{calc}(s,r) dr cell
where
 s
 vector of translation
 I
 integral
 R_{obs}
 observed electron density
 R_{calc}(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(S2S1)) + F2'(h)*F2(h) + F1(h)*F2'(h)*exp(2pih(S1S2)) = P0(0) + P1(S2S1) + P1(S1S2)
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 S1S2.
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(!FobsFnew!)
data_structure_9ins _cell.length_a 100.000 _cell_length_b 100.000 _cell.length_c 100.000 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _symmetry.space_group_name_HM 'P 1 21 1' loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au 2 3 4 12.3 1.2 2 3 4 11.4 1.1 . . . . . . . . . . . . .
For intensities use:
_refln.intensity_meas _refln.intensity_sigma
data_9ins _cell.length_a 100.000 _cell_length_b 100.000 _cell.length_c 100.000 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _symmetry.space_group_name_HM 'P 1 21 1' loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_au_sigma _refln.phase_calc _refln.fom 1 0 0 3468.4934 138.7397 0.746 1.000 2 0 0 618.4012 24.7360 11.948 1.000 . . . . . . . . . . . . . . . . . . . . . . . . . . .
Phases are in degrees.
HEADER R2SARSF 15JAN91 COMPND RIBONUCLEASE SA (E.C.3.1.4.8) COMPLEX WITH 3'*GUANYLIC ACID SOURCE (STREPTOMYCES $AUREOFACIENS) AUTHOR J.SEVCIK,E.J.DODSON,G.G.DODSON CRYST1 64.900 78.320 38.790 90.00 90.00 90.00 P 21 21 21 8 CONTNT H,K,L,S,FOBS,SIGMA(FOBS) FORMAT (2(I3,2I4,2F7.0,F6.0,9X)) COORDS 2SAR REMARK 1 TWO REFLECTIONS PER RECORD. REMARK 2 DMIN=1.85, DMAX=16.28 CHKSUM 1 MIN H=0,MAX H=34,MIN K=0,MAX K=41,MIN L=0,MAX L=20 CHKSUM 2 TOTAL NUMBER OF REFLECTIONS=17346 CHKSUM 3 TOTAL NUMBER OF REFLECTION RECORDS=8673 CHKSUM 4 SUM OF FOBS=0.235499E+07 0 0 3 60 9 16 0 0 4 106 307 25 0 0 5 166 23 20 0 0 6 239 657 52 0 0 7 326 0 38 0 0 8 425 511 40 . . . . . . . . . . . . . . . . . . . . . .
In this case the assumption is that order of data is H,K,L,F,sig(F)
2 3 4 12.3 1.2 2 3 4 11.4 1.1 . . . . . . . . . . . . . or 2 3 4 12.3 2 3 4 11.4 . . . . . . . . .
The length of file records must not exceed 80 characters. The format of the records is free, e.g. data must be separated by blancs (be careful  some PDB files do not satisfy this rule).
(see also Testing_program_MOLREP as tutorial)
#  molrep f fobs.dat m mm1.crd i <<stop #  # _NP 8 _RAD 27 _ANISO C _sim .1 _compl .5 stop
#  molrep f fobs.dat i <<stop #  _RAD 27 stop
#  molrep f p1.mtz m p1_pdb.pdb i <<stop #  _F FO _SIGF SDFO _NP 8 _ANISO C _sim .1 _compl .5 stop
For searching in the electron density map for some model (standard Rotation Function will be used):
#  molrep f p1.mtz m mod.pdb i <<stop #  _F FO _SIGF SDFO _PH PH_FO _NP 8 stop
#  molrep m mod1.pdb mx mod2.pdb i <<stop #  _PRF Y stop
#  molrep f fobs.dat m mod1.pdb i <<stop #  _dyad y _axis 0,10 _dist 0,300,300 _NPT 3 _NPTD 3 stop
#  molrep f fobs.dat m mod1.pdb i <<stop #  _dyad y _axis 180,10 _dist 0,300,1 _NPT 3 _NPTD 3 stop
#  molrep f fobs.dat m mod1.pdb i <<stop #  _dyad y _axis 180,10 _dist 0,300,1 _NSRF 20 _NPT 3 _NPTD 3 stop
#  molrep f mtz.mtz m 1hpg.pdb s new.seq i <<stop #  _F FP _SIGF SIGFP _NP 8 _NMON 2 _sim .1 _compl .5 stop
Program supports the point group symmetry.
NCS_ID  Point group description. 

N00 
Point group is N. For example Point group is 7, NCS_ID is 700. Standard orientation: Nfold axis along Z. 
N20 
Point group is N2. For example Point group is 72, NCS_ID is 720. Standard orientation: Nfold axis along Z, twofold axis along X. 
N22 
Point group is N22. For example Point group is 422, NCS_ID is 422. Standard orientation: Nfold axis along Z, twofold axis along X. 
230 
Point group is 23. Standard orientation: twofold axis along Z, another twofold axis along X. 
432 
Point group is 432. Standard orientation: fourfold axis along Z, another fourfold axis along X. 
532 
Point group is 532. Standard orientation: fivefold axis along Z, projection closest (to Z axis) threefold axis in plan XY along X. 
Polar angles theta, phi, chi define the standard system orientation in the cell. Theta, phi  polar coordinates of Z standard axis. Chi  angle of rotation around thetaphiaxis (Z standard axis) which bring X axis to standard X axis.
cx,cy,cz (fract.units) define the position of group centre in the cell.
It is possible to define NCS parameters using keywords or in input PDB file.
Input PDB file must contain only one molecule.Use keywords:
NCS, ANGLES, CENTRE
NCS  NCS_ID
ANGLES  theta, phi, chi
CENTRE  cx,cy,cz
First (reference) molecule must be started with line (free format):
#MOLECULE NCS_ID theta phi chi cx cy cz
Other molecules must be started with line:
#MOLECULE Nmol theta phi chi
where:
Nmol  molecule number.
theta phi chi  Polar angles of rotation from first molecule to current one.
For example: point group is 3.
HEADER HYDROLASE (ENDORIBONUCLEASE) CRYST1 64.900 78.320 38.790 90.00 90.00 ... #MOLECULE 300 0 0 0 .5 .5 .5 #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 ... ... #MOLECULE 2 0 0 120 #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 ... ... #MOLECULE 3 0 0 240 #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 ... ...
Alternative way is to use only first molrecule (with NCS parameters in the file) and generate complete model automaticly. In pure RB refinement use keyword DOM = 'C'. For fitting model into map (i.e. SAPTF+PRF+PTF use keyword NCS = 1).
In command string you can use options: "po" and "ps".
For example:
Usual MR with sequence and redirect output and scratch files molrep f file.mtz m model.pdb s file_seq po out/ ps scr/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 axisConvention for Orthonormal coordinate system
Orthonormal axes are defined to have: A parallel to X , Cstar parallel to Z