
MOLREP (CCP4: Supported Program)NAMEmolrep  automated program for molecular replacementSYNOPSISmolrep [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]
DESCRIPTIONVersion 7.2 /26.02.2002/FEATURES
CONTENTS
REFERENCESAuthor: 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. INPUT/OUTPUT FILESInput file
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
also (if you used keyword FILE_S):
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) ! + Multicopy search + + two different ! for MR ! 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) ! ! ! + Search model orientation in electron density map for particular position by phased RF (PRF=P) where: FUN, DYAD, PRF, LOCK  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
* Standard molecular replacement methodThe 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. Instead of computing RF, the program can use a list of orientations from a Rotation function which was prepared before. Anisotropic correction of data before computing RF can be useful for data with high anisotropy. 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: FobsFmod2*(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. Also in this case the possibility to choose from symmetryrelated models closest to which was found before is useful. The program can detect and use pseudotranslation vectors. In this case the pseudotranslation related copy will be added to the final model. The Packing function is very important in removing wrong solutions which correspond to overlapping symmetryrelated or different models.
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 onlyIf you define only a file of structure factors (Fobs), the program will compute a Self Rotation function with cutoff radius RAD = 30 as default. Use keyword RAD if you want another value. Other useful keywords: RESMAX, RES_R, COMPL, SIM. Resulting output:
* Search model in electron density mapIn 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.
Other useful keywords: COMPL, NMON, NP, NPT, RAD, RESMAX, SIM, SURF, INVER * Search model orientation in electron density map for particular position by PRFYou 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 * 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:
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.
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 modelThis 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 Rfactor and a Correlation Coefficient. Other useful keywords: COMPL, RESMAX, RES_T, SIM * Multicopy searchThere are two modes: "dyad_search" and "Multicopy 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:
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 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_TSR). 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. 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 correctionYou can improve your model beforehand by using keyword SURF. * Using sequence alignmentAnother 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 ! 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. The results of the alignment are written to the DOCfile, if this was defined. Without an Fobs file, the program only performs model correction. * NMR ModelYou 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 * EM or electron density modelSearching 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/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 FunctionLocked 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 refinementIf 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 HOW TO USE MOLREPA 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 aheadSuccess of the molecular replacement method depends on:
Things to look out for:
PseudotranslationMOLREP 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 Flexible modelIf 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 modelsIf 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
KEYWORDED INPUTThe available keywords are:
General keywordsLABIN <program label>=<file label>...Specify input column lables. The program labels defined are: F, SIGF, F(), SIGF(), I,SIGI, I(), SIGI(), PHIC, FOM
DOC < N  Y  A >Default: <N> use the additional file with the protocol of the running of the program: DOCfile molrep.doc
The DOCfile contains the protocol of the running of the program. NP <np>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. NPT <npt>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. NMON <nmon>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. COMPL <compl>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. SIM <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.
The use of Boff and Badd means to change Fobs and Fmodel: Fnew = Finput *EXP(Badd*RSQ)*(1EXP(Boff*RSQ) FUN < A  R  T  S >Default: <A>
FILE_T <filename>Default: <molrep_rf.tab> Input or output TAB_file (see also molrep_rf.tab) SURF < N  Y  A  O  2 >Default: <Y> Perform model correction.
RAD <rad>Default: automatically calculated from the model, unless:
Cutoff radius for Patterson search or for electron density search. RESMAX <resmax>Default: <3> High resolution limit. Keywords for special casesPST < N  Y  C >Default: <N> How to deal with pseudotranslation.
VPST <vpst1,vpst2,vpst3>Default: automatically from Patterson Pseudotranslation vector (in fractional units), used when PST = Y. MODE <F  S  M>Default: <F>
RES_R <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 <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 <badd>Default: <0> Fnew = Finput *EXP(BADD*RSQ)*(1EXP(BOFF*RSQ) ANISO < N  Y  C  S  K >Default: <N>
PACK < Y  N >Default: <Y>
LMIN <lmin>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. LMAX <lmax>Default: automatic choice Maximum Lindex of spherical coefficients. Possible values are 2,4,6,8,...,58,60. PRF < N  Y  S  P >Default: <N>
Program wiil 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 <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: <S>
DIFF < N  P  F >Default: <N>
P2 <p2>Default: <0> Percentage of model_2 in the structure. NREF <ncycle>Default: <10> number of cycles of rigid body refinement for each TF solution. (working only with MODE = S) see keyword:MODE NREFP <ncycle>Default: <0> number of cycles of rigid body refinement before TF for each peak RF. Default is without this refinement STICK < N  Y >Default: <N> Choose from symmetryrelated models closest to which found before (this option does not work with pseudotranslation possibility). FILE_S <filename>File with sequence for model correction by sequence alignment. NMR < 0  1  2  3 >Default: <0>
LOCK < Y  N >Default: <N> Locked Cross Rotation function will be performed. Use also keywords: FILE_TSR and NSRF Keywords specific for multicopy searchDYAD < N  Y  D >Default: <N>
DIST <Dmin,Dmax,Dpar>Three distances for dyad search.
AXIS <Chi,Delta>Default: <0,0>
NSRF <nsrf>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_TSR which must be prepared in advance (see Self Rotation Function). NPT <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 intermolecular vector search. If keyword DYAD is not given, the standard meaning of keyword NPT is used. NPTD <nptd>Number of peaks in TF to be checked through Correlation Coefficient calculations, for dyad search. NP2 <np2>Number of peaks in RF for second searching model to be checked for dyad search. FILE_M2 <filename>file of second searching model FILE_T2 <filename>file with list of peaks of RF for second searching model ALL < N  Y >Default: <N> if ALL = Y , program will use all Crystallographical Symmetry Operators Keywords for Self Rotation FunctionWithout a file of the model, the program computes a Self Rotation Function. CHI <chi>Default: <60> Angle chi of additional fourth section of RF(theta,phi,chi). SCALE <scale>Default: <6> Maximum value of RF is SCALE * SIGMA(RF). FILE_TSR <filename>Default: <molrep_srf.tab> Input or output TAB_file with peaks of Self_RF. Keywords for EM or electron density as model:DSCALEM <scale>Default: <1> scale factor of correction of density cell INVERM < N  Y >Default: <N> If Y , inverted phases will be used ROLIM <limit>Default: <not used> minimal value of density which will be used DRAD <radius>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 <vector>Default: <0,0,0> center of the model in the cell (in fract.units) Keywords for EM or electron density instead of Fobs:DSCALE <scale>Default: <1> scale factor of correction of density cell INVER < N  Y >Default: <N> If Y , inverted phases will be used DLIM <limit>Default: <not used> minimal value of density which will be used MOLECULAR REPLACEMENT METHOD  THEORYMolecular 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. ROT(R) = I P_{obs}(r) * P_{calc}(R,r) dr rad where
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
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.
Scaling by PattersonFor 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 (Boff)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= 4resmin^{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. The use of a priori knowledge of similarity and completeness of the modelFor 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. Functions of electron density searching (SM)We suggest a new approach to divide a phased sixdimensional search into three steps:
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 R_{obs}(r,s) * R_{calc}(r) dr rad(s) where
Phased Rotation function (PRF)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
Phased Translation function (PTF)Translation search in electron density map. PTR(s) = I R_{obs}(r) * R_{calc}(s,r) dr cell where
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:
Special Translation Function (STF) for dyad searchMulticopy searchSearch two copies of a model simultaneously. There are three stages to this:
Special Translation Function (STF)Imagine two models in the asymm. part of the unit cell:
Let
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. Anisotropic correction and scalingAniso 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!) COMMAND FILE EXAMPLESexample 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 phasesFor 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 PHIC=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 SelfRF 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_SRF 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 rotationRotation 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 systemOrthonormal axes are defined to have: A parallel to X , Cstar parallel to Z MEMORY CONTROL PARAMETERSIn 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 