Author: A.A.Vagin
email: alexei@ysbl.york.ac.ukYou 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 but if this file does not have such information, it will be taken from the coordinate file. In this case the input PDB coordinate file must contain correct CRYST1 cards with unit cell parameters and space group name for the unknown structure. You can change the space group of the structure factor file by using keyword NOSG.
"Sol_ 23 10.0 22.2 40.0"
"Sol_ 23 10.0 22.2 40.0 .564 .443 .032"
Some output files will not be deleted if keyword LIST=L. They have the internal format of the BLANC program suite and can be used by programs of this suite (see file README from ftp site: ftp.ysbl.york.ac.uk (user: anonymous, then: cd pub/alexei)
also (if you started from MTZ file):
also (if you used keyword FILE_S):
+-- Self RF (FUN=R, without any model)
!
+-- Standard MR -+-- Cross RF (FUN=A or FUN=R )
! !
! +-- 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, PRF and PTF
! (PRF=Y)
!
! +-- RF and PTF
! ! (PRF=N)
+-- Searching in ED map -+
! !
! +-- SAPTF, PRF and PTF
! (PRF=Y)
!
+-- Rotate and position the model (FUN=S)
where: FUN, DYAD, PRF - keywords
MR - Molecular Replacement
RF - Rotation function
TF - Translation function
PRF - Phased Rotation function
PTF - Phased Translation function
SAPTF - Spherically Averaged Phased Translation function
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 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:
||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. The program can detect and use pseudo-translation vectors. In this case the pseudo-translation related copy of the model will be added to the initial one.
The Packing function is very important in removing wrong solutions which correspond to overlapping symmetry-related or different models.
Use keywords:
COMPL, DIFF, FUN, MODEL_2, NMON, NP, NPT, P2, PACK, PST, RAD, RESMAX, SIM, STICK, SURF, VPST
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 to use keyword PHASE for BLANC file of phases.
- with keyword PRF = 'N' (default value):
the program applies standard molecular replacement calculations: Rotation function (in Patterson space) 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.
Other useful keywords:
COMPL, NMON, NP, NPT, RAD, RESMAX, SIM, SURF
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):
the program applies standard molecular replacement calculations: Rotation function (RF) to search the orientation and Phased Translation function (PTF) to search position.- 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.
Other useful keywords:
COMPL, NP, NPT, RAD, RESMAX, 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 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.
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 keyword NSRF).
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 AXIS NP NSRF NPT NPTD NP2 FILE_M2 FILE_T2 NMON
and also:
COMPL SIM RESMAX SURF
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 superimosed before. Algorithm is equivalent to sum RF or/and TF for individual structures. 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
A simple way to use MOLREP is to define files for Fobs and the model, number of model to search, 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. Keywords with short explanations are printed by the program at the beginning of execution. However, the program automatically produces a batch command file during dialogue. This feature might be useful for repeated calculations.
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 add to the model a copy of model which is translated by the pseudo-translation vector.
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
It is easy to use MOLREP interactively, but can be used in batch. All keywords must be preceded by an underscore (e.g. _DOC). The available keywords are:
These three keywords always must be defined in this order:
DOC
FILE_F
FILE_MIf you use MTZ file you have to put MTZ keywords after FILE_F Ahd finish it with line "_END".
General keywords
Common:
FILE_T, FUN, NMON, NP, NPT, RADAnd for structure factors control:
COMPL, RESMAX, SIMAnd for model control:
MODEL_2, SURFAnd for multi-copy search:
DYAD, FILE_M2, FILE_T2, NP2, NPTD, NSRFAnd for search in ED:
PHASE, PRFAnd for fitting two models:
PRFKeywords 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, VPSTAnd for Self RF:
CHI, PST, SCALEAnd for multi-copy search:
AXIS, DIFF, DIST, NMR P2And for search in ED:
DIFF, P2, NPTDAnd for fitting two models:
NPTD
To get started with MOLREP, you first have to answer three questions:
Do you want to have FILE-DOCUMENT molrep.doc? < N | Y | A >
Default: <N>
The DOC-file contains the protocol of the running of the program. With the DOC-file, the program creates a command (batch) file: molrep.bat.
What is the name of the input file with Fobs (allowed formats: ASCII (CIF or PDB) or BLANC or MTZ), i.e. FILE_F?
Assign the name of a formatted file of structure factors, or, in the case of fitting two models, leave this option out. When using an MTZ file, here MTZ keywords must be used.
What is the name of the input file with the model coordinates (allowed formats: PDB, CIF or BLANC), i.e. FILE_M?
The unit cell and space group of this file must be the same as those for the file with Fobs (of the unknown structure). If they are not the same, the program will take these values from the Fobs file.
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
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*RSQ)*(1-EXP(-Boff*RSQ)
Default: <A>
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.
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.
Default: automatically from Patterson
Pseudo-translation vector (in fractional units), used when PST = Y.
Default: <F>
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*RSQ)*(1-EXP(-BOFF*RSQ)
Default: <N>
Default: <Y>
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>
Default: none
If you want to use phases from CIF or MTZ, use "+" or "-" ("-" means inverted phases will be used). The CIF or MTZ file must contain phases and you have to use relevant keywords for MTZ.
If you want to use a BLANC file of phases, use "+name" or "-name", where "name" is the name of the file with phases. Again, "-" means inverted phases will be used.
If keyword PRF is N, a standard Rotation Function (RF) and Phased
Translation function (PTF) will be computed.
If keyword PRF is Y, SAPTF, Phased Rotation Function (PRF)
and Phased Translation Function (PTF) will be computed.
Default: <0>
Number of new space group if you want to change the space group for the file of structure factors.
Default: <S>
Default: <N>
use ||Fobs|-|Fmod2|*(P2/100)|
use vector difference (Fobs - Fmod2*(P2/100))
Default: <0>
Percentage of model_2 in the structure.
Default: <N>
Choose from symmetry-related models closest to which found before (this option does not work with pseudo-translation or with dyad search).
File with sequence for model correction by sequence alignment.
Default: <0>
Default: <N>
Three distances for dyad search.
Default: <0,0>
Default: <0>
Number of peaks of Self-RF which will be used instead of Chi rotation. 0 means not to use Self-RF. A list of Self-RF peaks will be taken from file molrep_srf.tab, 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
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).
The best and easiest way to prepare a command file is to run MOLREP once by dialogue. If a molrep.doc file was assigned, the program creates a command (batch) file (molrep.bat) automatically.
See some command (batch) file examples.
The following keywords are necessary only for MTZ files.
Label of F or F(+)
Label of sigma F or sigma F(+)
Label of F(-)
Label of sigma F(-)
Label of I or I(+)
Label of sigma I or sigma I(+)
Label of I(-)
Label of sigma I(-)
Label of phases
Label of figure of merit
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 scaling of two Patterson maps. This method makes it possible to have a very 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.
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_H-M '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_H-M '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 15-JAN-91
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).
# -------------------------------- molrep <<stop # -------------------------------- # _DOC Y # _FILE_F fobs.dat _FILE_M mm1.crd # # _NP 8 _RAD 27 _ANISO C _sim .1 _compl .5 _END stop
# -------------------------------- molrep <<stop # -------------------------------- # _DOC Y # _FILE_F fobs.dat _FILE_M # # _RAD 27 _END stop
# -------------------------------- molrep <<stop # -------------------------------- # _DOC Y # _FILE_F p1.mtz # _F FO _SIGF SDFO _END <--- end of MTZ block # _FILE_M p1_pdb.cds # # _NP 8 _ANISO C _sim .1 _compl .5 _END stop
For searching in the electron density map for some model (standard Rotation Function will be used):
# -------------------------------- molrep <<stop # -------------------------------- # _DOC Y # _FILE_F p1.mtz # _F FO _SIGF SDFO _PH PH_FO _END <--- end of MTZ block # _FILE_M mod.pdb # # _NP 8 _PHASE + _END stop
# -------------------------------- molrep <<stop # -------------------------------- # _DOC Y # _FILE_F _FILE_M mod1.pdb # _MODEL_2 mod2.pdb _PRF Y _END stop
# -------------------------------- molrep <<stop # -------------------------------- # _DOC Y # _FILE_F fobs.dat _FILE_M mod1.pdb # _dyad y _axis 0,10 _dist 0,300,300 _NPT 3 _NPTD 3 _END stop
# -------------------------------- molrep <<stop # -------------------------------- # _DOC Y # _FILE_F fobs.dat _FILE_M mod1.pdb # _dyad y _axis 180,10 _dist 0,300,1 _NPT 3 _NPTD 3 _END stop
# -------------------------------- molrep <<stop # -------------------------------- # _DOC Y # _FILE_F fobs.dat _FILE_M mod1.pdb # _dyad y _axis 180,10 _dist 0,300,1 _NSRF 20 _NPT 3 _NPTD 3 _END stop
# -------------------------------- molrep <<stop # -------------------------------- # _DOC Y # _FILE_F mtz.mtz # _F FP _SIGF SIGFP _END <--- end of MTZ block # _FILE_M 1hpg.pdb # # _NP 8 _NMON 2 _FILE_S new.seq _sim .1 _compl .5 _END stop
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.f or 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 enough memory ...
change parameter MEMORY in main_molrep.f or in main_molrep_mtz.f for CCP4 version of MOLREP.
There are only 2 subroutines dependent on operating system in the file molrep_unix.f:
(both are not very important for calculations)
You need to uncomment corresponding operators in these subroutines. For example:
C
C SUBROUTINE DISPL_BL(LINE)
C C
C C -P- DISPL - write message to terminal and stop cursor
C C at the end of line.
C C
C CHARACTER LINE*(*)
C INTEGER*4 NL
C CALL LENSTR_BL(LINE,NL)
C IF(NL.GT.79) NL=79
C CVX WRITE(*,'(''$'',A)') LINE(1:NL)
C CDP WRITE(*,'('' '',A,$)') LINE(1:NL)
C CMS WRITE(*,'('' '',A,\)') LINE(1:NL)
C CLN WRITE(*,'('' '',A,$)') LINE(1:NL)
C RETURN
C END
C
C CVX - for VMS VAX
C CDP - for unix system
C CMS - for MS-DOS
C CLN - for Linux
C
C
C SUBROUTINE CLOCK(IH)
C
C -P- CLOCK - get date to --> array IH()
C
C IH(2),IH(3),IH(4), IH(5),IH(6),IH(7)
C sec min hour day month year
C
C INTEGER*4 IH(7)
C ******
CMS INTEGER*2 IHR,IMN,ISEC,I100H,IYR,IMON,IDAY
CVX CHARACTER STR*8
CDP INTEGER*4 ID(3)
CLN INTEGER*4 ID(3)
C --------------------------------
C
CVX CALL IDATE(I1,I2,I3)
CVX IH(5)=I2
CVX IH(6)=I1
CVX IT1 =I3+2000
CVX IH(7)=IT
CVX CALL TIME(STR)
CVX READ(STR,'(I2,1X,I2,1X,I2)') IH(4),IH(3),IH(2)
CVX IH(1)=0
C
C
CMS CALL GETTIM(IHR,IMN,ISEC,I100H)
CMS CALL GETDAT(IYR,IMON,IDAY)
CMS IH(4)=IHR
CMS IH(3)=IMN
CMS IH(2)=ISEC
CMS IH(5)=IDAY
CMS IH(6)=IMON
CMS IH(7)=IYR
CMS IH(1)=I100H/2
C
CDP
CDP CALL ITIME(ID)
CDP IH(4)=ID(1)
CDP IH(3)=ID(2)
CDP IH(2)=ID(3)
CDP CALL IDATE(IMON,IDAY,IYR)
CDP IYR=IYR+2000
CDP IH(5)=IDAY
CDP IH(6)=IMON
CDP IH(7)=IYR
CDP IH(1)=0
CDP
C
C
CLN
CLN CALL ITIME(ID)
CLN IH(4)=ID(1)
CLN IH(3)=ID(2)
CLN IH(2)=ID(3)
CLN CALL IDATE(IMON,IDAY,IYR)
CLN IYR=IYR+2000
CLN IH(5)=IDAY
CLN IH(6)=IMON
CLN IH(7)=IYR
CLN IH(1)=0
CLN
C
C
C RETURN
C END