The BLANC program suite is a collection of programs which can be used for macromolecular structure determination by X-ray crystallography. The suite is designed to provide experienced crystallographers and students with a number of simple tools. Beside set of small programs, the BLANC system introduces so-called superprograms which represent larger programs composed of several smaller programs. They utilize so-called black-box principle requiring minimum preparations or intervention from a user. The programs are written in standard Fortran77. They are connected by standard BLANC data files.
Authors: A.A.Vagin, G.N.Murshudov, B.V.Strokopytov
email: alexei@ysbl.york.ac.uk
Main reference:
A. A. Vagin, G. N. Murshudov and B. V. Strokopytov
BLANC: the program suite for protein crystallography
J. Appl. Cryst. (1998). 31, 98 - 102
References:
Vagin, A.A. Ph.D. Thesis, Institute of Crystallography, Moscow, 1983.
Vagin, A.A. New translation and packing functions., Newsletter
on protein crystallography., Daresbury Laboratory, number 24, 1989.
A.A.Vagin, G.N.Murshudov, B.V.Strokopytov
The BLANC program suite for Protein Crystallography.
Newsletter on protein crystallography., Daresbury Laboratory,
(1997) 33, pp 25-30.
A.Vagin,A.Teplyakov, A Translation-Function Approach for Heavy-Atom
Location in Macromolecular Crystallography. Acta Cryst. (1998).
D54, 400-402
A.Vagin,A.Teplyakov, MOLREP: an automated program for
molecular replacement., J. Appl. Cryst. (1997) 30, 1022-1025.
A.A.Vaguine, J.Richelle, S.J.Wodak. SFCHECK: a unified set of
procedure for evaluating the quality of macromolecular stracture-factor
data and their agreement with atomic model.
Acta Cryst.(1999). D55, 191-205
Copy file blanc.tar.gz
and uncompress it (`gunzip blanc.tar.gz')
After untaring ( command: tar xvf blanc.tar ) `blanc.tar' , you will get a blanc directory, with ccp4, doc, dic, example, exe, for, mappage, mmm, lib, prog, start, start, sfcheck, molrep, makecif, contact, mir directories and file README
Compilation.
All executable files will finish up in the exe directory. CCP4 version of some programs will be prepared automaticly if ccp4 is installed. For details look at BLANC manual in the file: blanc/doc/blanc_descr.txt Also useful program BLANC_HELP which gives list of blanc's programs with short description.
- All programs demand minimal necessary parameters. Most of them have
default values and can be put into the program by pressing CR.
- It is possible to use programs in dialogue mode or in batch mode.
Modern computing thecnology allows to carry out most of the calculations
for small and medium sized proteins in real time, therefore, dialogue
is a preferable way of running programs in the BLANC program system.
However, each program automatically produces a batch command file
during dialogue. This feature might be useful for repeated calculations.
- Program parameter requests are self-understandable because
there are short prompts with explanations.
- If necessary it is possible to use keywords to change certain
parameters. Keyword are printed by the programs at the beginning
of execution.
Most of BLANC programs do not require large memory. All BLANC programs
are written in standard FORTRAN codes and can be running at least by
VMS VAX, UNIX.
Original features
BLANC contains a set of new original algorithms and programs developed
independently by us. Among them algorithms for calculation of translation
and packing function (Vagin, A.A., 1983; Vagin, A.A. 1989), new program for
data scaling using Patterson origin peak (will be published eslewhere),
program for black-box molecular replacement, black-box heavy-atom search and
phasing, global omit map program (Vagin, A.A., unpublished results) and
others.
Additional notes:
1. BLANC was created in 1979 in Institute of Crystallography in Moscow.
Fortunately general initial construction was goud enough and we
have the same in this time. Only two things were changed. First,
in the begining there was main program which gather all program -
subroutines in the single program. Second, there was "sum-file"
which looked like MTZ-file of CCP4. This file gathered apmlitudes
and phases of native structure and derivatives. After 5 years
expirience we refused of it. A lot of structure was solved to use
these programs and now we have programs which cumulated expirience
solving these structure. Main feature of new version BLANC is
introducing super-programs.
2. Super-programs - It is better to start to work with BLANC by super-
programs. Each super-program runs as black-box. Usually this box uses
a lot of programs ( subroutine version ) with several default
parameters. These defaults accumulated the expirience of author
about this subject. Text of super-program is short. It looks like
a collection of small boxes with definition its parameters. Test of
super-program exactly corresponds to flow-chart which you can find in
Appendix A.So it is convinient to learn the method. Of course you can
repeate the calculation a program by program and use another values of
parameters or another program. After that you will have own
modification of the method. If you put the programs (subroutine
version) which were used with its parameters into the single program
you will have new super-program.
3. Memory request.
The programs in the super-programs use common working array which
size is easy to change because only one or two parameters control
it.
4. NC-symmetry.
The files of coordinates contains information about asymmetric part
of unit cell and non-crystallographic symmetry. Some programs need
to use the non-crystallographical symmetry operators when it is
necessary to restore the contents of asymmetrycal part of unic cell.
In this case information will be taken from coordinate file. In
other cases programs do not use this information and do not check it.
5. FFT
Calculation the structure factors and the density produced by FFT for
all space groups.
6. Phases - BLANC uses two kinds of representation of phases:
1. by angles - mcos(phi),msin(phi) , where m - figure of merit
2. by Hendrickson_Lattman coefficients ABCD.
You can have HL cofficients:
1. from program PHASE for heavy atom derivative.
2. to transform the phases by program PHABCD.
You can transform HL coefficients to the phases by program ABCDPH.
Coefficients ABCD are very usefull to combine phase information. You
can do it by programs ABCDPH.
7. Boff - soft low resolution cut-off.
Disordered solvent contributes to diffraction in the low resolution
range. To avoid influence of solvent usual prartice is to apply
low resolution cut-off (~8A). Low resolution cut-off introduces
systematical errors in the electron density especially near the
surface of the model. It is the series termination effect. Instead to
use of usual low resolution cut-off program multiplies the modules
of structure factors by special coefficient:
Fnew = Fold (1-exp(-Boff*s^2)) , where Boff= 4resmin^2
This is a kind of to remove the desordered solvent influence. There
are several algorithms trying the modeling the solvent. Usual way is
to apply additional coefficient like which this program uses. But it
is not possible to have correct model of solvent without special
experement to registrate diffuse scattering and it seems a good idea
is just to remove structure factors in this resolution range by
"soft low resolution cut-off".
8. Patterson scaling.
Scaling and the estimation the overall thermal factor. Scaling by
Wilson plot is rather difficult because the distribution of amplitudes
is not Wilson's distribution especially for low resolution
data. Program estimates the overall thermal factor by the origine
peak of Patterson which always looks like a gaussian. It makes the
estemation much more easy. This method makes possible to have good
aproximation even for low resolution data where other methods don't
work. Scaling observed and calculated amplitudes is making by the
comparison of its the origine peaks of Patterson.
9. Completeness. Missing some data means to use its with value
equal 0. Better aproximation for such data is the average value for
corresponding resolution shell. Because program scales the
data by Patterson this average value always is more realistic.
10. News.
In directory blanc/doc there is file "news" which describes recent
changes of BLANC.
11. If you have CCP4 package you can read MTZ file and prepare
CIFile by program MTZ2CIF which uses libraries of CCP4.
Also you can prepare CCP4 version of SFCHECK,MOLREP,MIR
See file compl.bat in directory: blanc/start/unix
Program Function
A. Entrance and exit.
readPDB converts PDB cooordinates file to BLANC/CIF
writePDB converts cooordinates to PDB file
TOBLANC converts structure factors & phases to BLANC format
FROMBL converts structure factors & phases to CIF
The exit from program suite BLANC.
F2CIF writes a contents of internal BLANC files: Fobs,
Fcalc, Phases to one output formatted CIFile.
The exit from program suite BLANC.
B. Fourie transformation.
COEF calculates various kinds of Fourier coefficients
FFT calculates maps using FFT
RFT calculates structure factors
REDUCT check asymmetric part, other part will be
equaled to zero.
CFFT COEF (without anom. scatt.) + FFT
RFFT REDUCT + RFT : fast fourie transform:
real --> complex.
SF_CALC computes Structure factors by formula for
atomic model, can use atomic aniso B factors.
C. Look up.
LOOKFL internal files lookup
PRINTD converts maps to simple ASCII file
ISOLINE draws maps in isolines (Postscript format)
RSOLINE draws maps of self-rotation function
in isolines (Postscript format)
D. Statistics.
FLSTAT gives various statistics for structure factors
files, etc.
MODCHECK gives statistics about restraints
E. Scaling.
SCALE calculates Wilson plot scale
PSCALE Patterson origin peak scaling
ANISOSCL calculates anisothermal scaling of two files
F. Modification, copy and merge.
MODDEN density modification program
COPYFL changes file titles, scale, etc.
CONCRD modifies cooordinate files
JOINFL merges the files of structure factors,
phases or Hendrickson-Lattman coefficients.
TRANS transforms atomic coordinates.
SORTMRG reads, sorts, averages the files of
structure factors or phases
JOINCRD merges two files of coordinates
G. Molecular replacement.
RFCOEF calculates coefficients of spherical harmonics
RFRES calculates Rotation Function (Euler angles)
RFROT calculates rotated spheric coefficients
RFADD adds spheric coefficients
TRPACK 3D translation/packing/phased translation function
RTRANS transforms Rotation Function map to polar angles
ANGSUM computes the sum of two euler angles
H. Isomorphous replacement.
PHASE calculates Henrickson-Lattman coefficients
for a derivative
REFINE heavy atom's full matrix refinement
J. Refinement.
ROTLSQ rigid body refinement
also as PATLSQ - refines oriention of a model
before translation function search.
ROTFFT rigid body refinement by FFT
K. Others.
ABCDPH calculates phases of structure factors
from Henderickson-Lattman coefficients
ALIGN alignes optimally 2 aminoacid sequences
BLANC_HELP gives list of blanc's programs with short description.
CHECK_CRD gets information about file "crd"
CREAT_INF creats INF_file
CONDEN reshuffles 3-d electron density map
CONSEQ converts sequence to coordinate file
CONTACT computes inter or/and intra molecular contacts
DNS2CCP4 converts density map to CCP4 format
EXTRACT creats density map around model.
FIT superimposes two sets of coordinates
FMINUSF creats file with Fnew = ! !F1! - scale * !F2! !
FPLUSFOM transfers values of Figure-Of-Merit from "phase"
to "amplitude" file.
FRAGSRCH builds full atomic model of a protein using
C-alpha atom coordinates
GENDEN generates electron density
GENDEN_ANISO generates electron density for atomic
model with aniso B factors.
GENIND generates the full list of indices
HISTOGRM histogram matching
MTZ2CIF reads MTZ file of CCP4
BLANC2MTZ creates new MTZ file with Fobs, Fcalc and Phases
PEAKSRCH performs map peak search
PHABCD calculates Henderickson-Lattman coefficients
for calculated phases using observed and
calculated amplitudes
SFVSUM sum two vectors of structure factors:
(F1 + scale*F2) or convolution: F1(h)*scale*F2(-h)
SURFACE calculates solvent accessible surface area
RANDCRD introduces a random errors to coordinates.
RANDF introduces a random errors to !F!
TWIN perfect and partial hemihedral twinning test,
can create output file with detwined data.
WATPEAKS perfomrs water peak search and water replacing
L. Not converted to current version yet.
SEQSRCH searches for a given aminoacid sequence in
the local Sequence Data Bank.
BBONE inserts side chains of a protein into
electron density map
GROUP converts scattering from protein atoms to
group scattering factors thus reducing time
for different refinements and searches at low
resolution
DPLOT draws PostScript stereo picture of the model
with electron density
SKELETON density skeletonisation procedure
LOCSCL anisothermal local scaling
Program Function
A. Isomorphous replacement method:
see also README in blanc/mir/
MIR * performs automated heavy atom search and phasing
for one or several derivatives. This program is based on
program TRAHALO which used translation function
approach for heavy atom solution.
* Program supports SAD,SIR,SIRAS,MIR,MIRAS cases.
* can use MTZ file as input.
* can use the phases from other sources.
* can manage pseudo-translation.
* can refine phases by density modification
/solvent flattening/
TRAHALO TRAslation function Heavy Atom LOcation.
* performs automated heavy atom search and phasing
for one derivative.
* Program supports SAD,SIR,SIRAS cases.
* can use the phases from other sources.
* can manage pseudo-translation.
/ also is the part of MIR /
MIR_II performs automated phasing: computes the phases of
native structure factors by using information of several
derivatives (structure factors and coordinates).
Can refines phases by density modification
/solvent flattening/
/ this program is auxiliary program, just refines
heavy atom position, computes ABCD coefficients
and combines its. /
B. Molecular replacement method:
see also README in blanc/molrep/ about MOLREP.
MOLREP performs automated molecular replacement search: for given
Fobs and atomic model creats new model coresponding
to the maximum of rotation and translation functions.
Program can check several peaks of rotation function
by computing each translation function, refine new model
and select result by correlation coefficient.
Program can use second fixed model with correct position
and orientation.
SELFROT calculates self-rotation function
CROSSROT calculates cross-rotation function
TRFUN calculates translation and packing function
C. Refinement:
see also README in blanc/makecif/ about MAKECIF.
MMM Macro Molecular Minimization/Crystallographic
refinement. Minimizes difference between observed electron
density map and map of atomic model. Uses the restrains
files from program MAKECIF.
MAKECIF restrain maker.
uses as input CIF or PDB_file and libraries mon_lib.cif,
ener_lib.cif, symlib.blc and creates files:
1. with atomic coordinates, symmetry and unit cell
parameters. / file extension "crd"/
2. with chemical structure description and atomic
scattering structure factors. / file extension "str"/
3. with restraints: standard values of bonds, angles,
torsion angles, chirality centres, plan groups, its
actual values in the structure. / file extension "rst"/
If the description of a monomer is absent in the library
program will try to create library description and write
it to special file for further inclusion to the library.
Program creates PostScript files with the pictures of new
monomers.
Can read additional library of monomers.
MODCHECK restrain checker.
reads CIFiles of coordinates and restraints,
gives information about restraints (to DOC_file),
writes PDB_file or/and CIFile of coordinates.
LIBCHECK PDB/CIFiles, library manager.
reads library of monomers, performs various checks:
gives information about some monomer,
creates PostScript file with picture and information
about bonds, angles, ...
can read additional library, add two libraries and write to
a new library file ;
can create description of new monomer reading coordinates
from PDB file of CIFile.
EMIN performs energy minimization.
energy minimization / or B_factor regularization /
minimizes the energy of structure using the restraints
files from program MAKECIF.
E_total = E_bond + E_angle + E_tors + E_vdw + E_hb
E_bond = Sum ( Kb * (Bobs -Bidl)**2 )
E_angle = Sum ( Ka * (ANGLEobs -ANGLEidl)**2)
E_tors = Sum ( Kt * (PHIobs -PHIidl)**2 )
E_vdw = Lennard-Jones 6-12 potential
E_bond = 10-12 potential
DENMOD phase refinement by density modification
D. Others:
OMIT for given Fobs and atomic model computes omit-phases
which corresponds to omit map.
OMIT_MAP creats total omit map
SFCHECK checks quality of X-ray structures.
checks agreement PDB coordinates file and PDB structure
factors file; gives information about R-factor,
correlation, Luzzaty plot, Wilson plot, Boverall, ...,
local error estimation by residues. Can compute omit
phases and use its instead phases of model.
Possible use program for BLANC_coordinates file and
internal BLANC structure factors file.
1. FILE-DOCUMENT - The file for saving messages of program. Usually these
/formatted/ messages are the same that screen of terminal messages.
Sometimes this file contains additional information.
Extention of this file "doc".
If program creats DOC_file additional file with
extention "bat" would be created. This is batch_file.
It is possible to use it if you want to repeate to run
program.
2. INF-FILE - contains unit cell parameters, name of space group,
/formatted/ crystallographical symmetry operators,
non-crystallographical symmetry operators.
You can creat this file by program CREAT_INF. Program
create INF_file and as comments examles of BLANC file
of coordinates, formatted CIFile of structure factors,
phases, Henderson/Lattman coefficients. Usually all
internal files contains this information in the titles
but some programs need or may use this file.
Extention of this file "inf".
3. Internal files /unformatted/:
Modules of sructure factors, phase, coefficients, density:
Files type of
"F " contain indices and structure factors,
"FS " contain indices, modules of structure factors and sigmas,
"PH " contain indices, m*sin(alpha) and m*cos(alpha) (m is figure
of merit),
"ABCD" contain indices and Hendrickson-Lattman coeficients of
distrubition of phases,
"COEF" contain indices and coeficients of Forie transformation,
"RI " contain grid points and corresponding value of electron
density (see for example description in LIBUTILS),
"ALMN" contain indices and coeficients of rotation function.
ALL internal files contains in the titles the information about
unit cell parameters, name of spase group, crystallographical symmetry
operators and special information depending on type of file.
For example for density file : numbers of grid points,rms of
electron density. You can see the contents of these files by
programs: LOOKFL, FLSTAT, PRINTD. Extention of all these files "dat".
4. Atomic coordinates file and file of heavy atoms / formatted CIF/:
These file must have extention "crd".
Format of coordinate's file is very closed to CIF.
Difference is for the special cases:
1. when the non-cryst. symmetry is exist the some groups contain
the same chain related by non-cryst symmetry operators.
2. when some of groups lying in the special position are exist.
3. for file of heavy atom parameters
You can find more information and an example of coordinate's file
and file of heavy atoms in appendix C.
5. Output PDB_coordinates file:
This file created by program "writePDB" and would have extention "pdb".
6. Output file of structure factors / formatted CIF/:
This file created by program "frombl".
7. Intput PDB_coordinates file:
Thise file used by program "readPDB" and must have extention "pdb".
When you tape file name for program request you need not tape the
extention. Program add the extention automatically.
8. File converting.
1. PDB_file of coordinates may be converted to BLANC_file
by program "readPDB". PDB_file must contain HEADER,SCALE
and CRYST1 cards. MTRIX card is acceptable.
2. If you want to creat new file of coordinates, cread INF_file
by program "creat_inf" and see example in the comments.
3. Formatted file of structure factors may be converted to intenal
BLANC_file by program "toblanc". Input file must be
file with PDB-format or CIFile which contains indices
and structure factors or intensities or phases, (also simple
formatted file with "h,k,l,!F!,sig(F)" or "h,k,l,!F!"
and without titles is acceptable)
A. Example of CIfile of amplitudes:
data_structure_9ins
_entry.id 9ins
_struct.title ' insuline 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
2 3 4 12.3 1.2
-2 -3 -4 11.4 1.1
. . . . . . . . . . . . .
or just:
data_structure_9ins
loop_
_refln.index_h
_refln.index_k
_refln.index_l
_refln.F_meas_au
_refln.F_meas_au_sigma
2 3 4 12.3 1.2
-2 -3 -4 11.4 1.1
. . . . . . . . . . . . .
For intensities use:
_refln.intensity_meas
_refln.intensity_sigma
For phases use:
_refln.phase_calc
_refln.fom
B. Example of PDB file of amplitudes:
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
. . . . . . . . . . . . . . . . . . . . . .
C. Example of simple formatted file of amplitudes:
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 separeted by
blancs. ( be careful - some PDB files do not satisfy this rule)
Program uses the information about cell parameters and space
group from PDB coordinate file.
Program "creat_inf" creats several examples of input files.
1. You can find all information in directories:
+-- exe executable program codes
!
!-- example test files:
! "2sar.sf" - formatted PDB file of SF.
! "2sar.pdb" - PDB file of coords.
!
blanc --!-- for text of all programs.
!
!-- doc "blanc_descr.txt" .
!
!
+-- lib libraries: "libutils.ftn"( -->"libutils.a")
! "libsubr.ftn" ( -->"libsubr.a")
! "bl_graph.f" graphics subroutines
!
!
+-- dic "bank.frm" - for program "fragsrch"
!
!
+-- start "presubr.f"
! "prelib.f"
! "setup.unx"
! "compl.bat" batch_file for compilation all programs
!
!
+-- mappage "mappage.f","map_r.f" connection with "O".
! "map_prot.f,"map_asci.f"
!
+-- prog example-program: template-program for read/write
! read_atoms.f - model to memory
! read_crd.f - cordinates
! read_sf.f - file of !F!
! read_dns.f - density file
+-- temp
!
+-- makecif
!
+-- mir
!
+-- mmm
!
+-- sfcheck
!
+-- molrep
!
+-- contact
!
+-- ccp4 "mtz2cif" - reads MTZ file and prepares CIFile.
"dns2ccp4" - converts density map to CCP4 format
"ccp42dns" - converts CCP4 density map to BLANC map
"dns2ccp4" - writes a contents of BLANC files to MTZ file
Several programs and superprograms have independent from the BLANC
versions (SFCHECK, MOLREP, MIR, CONTACT, MAKECIF, EMIN, LIBCHECK etc.)
and are kept in separate directories. You can find more information in:
SFCHECK - blanc/sfcheck/README
MOLREP - blanc/molrep/README
CONTACT - blanc/contact/README
LIBCHECK !
MAKECIF !- blanc/makecif/README
EMIN !
MIR !
MIR_II !- blanc/mir/README
TRAHALO !
1. Get commands: a) "setenv BLANC path_name".
Example: "setenv BLANC ~alexei/blanc
or put it to your ".personal-cshrc"
b) "set path=($path ~alexei/blanc/exe)"
2. Testing.
There are two files for testing in the directory blanc/example.
"2sar.sf" - formatted PDB file of SF.
"2sar.pdb" - PDB file of coords.
2.1. Testing super_program SFCHECK:
a) go to directory blanc/example
b) run program "sfcheck" for files:
2sar.pdb - PDB_coordinate file
2sar.sf - file of structure factors
c) after that we wil have:
2sar.crd - BLANC_coordinate file
sfcheck.fob - BLANC_Fobs_file
sfcheck.fmd - BLANC_Fmodel_file
sfcheck.fsc - BLANC_Fmodel_scaling_file
sfcheck.ph - BLANC_PHASE_file
sfcheck.dn1 - BLANC_density_file
/ after program "genden" /
2.2. Testing super_program MOLREP:
see README in blanc/molrep/
2.3. Testing super_program MIR:
see README in blanc/mir/
Easy way to understand how to use BLANC subroutines is to look at
the example-programs in "blanc/prog" directory:
read_sf.f - read/write structure factor files
read_dns.f - read/write density files
read_crd.f - read/write coordinate files
reaf_atoms.f - read/write coordinate files and keep all atoms in memory.
1. There is common block for general structure description: /CRYSTL/
with cell parameters, space group definition, matrix to convert
fract. coordinetes to orthogonal and vice versa (FRTOCR,CRTOFR)
Some subroutines to control the content common block /CRYSTL/:
SET_CELL - put parameters to common/CRYSTL/,
calc reciprocal cell parameters,volume and calc matrix
FRTOCR and CRTOFR
GET_CELL - get parameters from common/CRYSTL/
REPCELL - using CELL parameters from common/CRYSTL/ calc reciprocal
cell parameters,volume and calc matrix FRTOCR and CRTOFR
2. Subroutines to read/write files of F, phases, ABCD, Almn coefficients.
This subroutines uses common blocks /COMRDF/ and /COMWRF/
for read/write title of file.
Some subroutines to control the content this common block:
C_RD_CR - copy information from common/COMRDF/ to common/CRYSTL/
also using CELL parameters from common/CRYSTL/ calculates
reciprocal cell parameters,volume and calc matrix
FRTOCR and CRTOFR
C_CR_WR - copy information from common/CRYSTL/ to common/COMWRF/
C_RD_WR - copy information from common/COMRDF/ to common/COMWRF/
GET_TITLE - get information from /COMRDF/
SET_TITLE - set information to /COMWRF/
SET_WRF - put N_SpGr, N_SETT, CODE_SpGr, CODE_PDB to common/COMWRF/
NAME_PDB, DATE_PDB , TITLE_PDB
read/write subroutines:
ORFILE - 1.open file.
2.reads title of file and copy file_parameters to /COMRDF/.
OPFILE - 1.don't open file, rewind file
2.reads title of file and copy file_parameters to /COMRDF/.
OWFILE - 1.open file.
2.writes title to file from common /COMWRF/
RD - read from file; type of file :"F ","PH ","COEF","ALMN"
RRD - read from file; type of file :"FS "
RD1 - read from file; type of file :"F ","PH ","COEF","ALMN"
RRD1 - read from file; type of file :"FS "
RD2 - read from file; type of file :"F ","PH ","COEF","ALMN"
RRD2 - read from file; type of file :"FS "
RD3 - read from file; type of file :"F ","PH ","COEF","ALMN"
RRD3 - read from file; type of file :"FS "
RD4 - read from file; type of file :"F ","PH ","COEF","ALMN"
RRD4 - read from file; type of file :"FS "
RABCD - read from file; type of file :"ABCD"
RABCD1 - read from file; type of file :"ABCD"
WRT - write to file; type of file :"F ","PH ","COEF","ALMN"
WWRT - write to file; type of file :"FS "
WRT1 - write to file; type of file :"F ","PH ","COEF","ALMN"
WWRT1 - write to file; type of file :"FS "
WABCD - write to file; type of file :"ABCD"
WABCD1 - write to file; type of file :"ABCD"
3. Subroutines to read/write density file:
Subroutines to read open file and use common block /COMRDF/ to keep
title
RDENS - reads density file, put current section of map to real array.
RDENS2 - reads density file, put current section of map to real array.
IRDENS - reads density file, put current section of map to integer array.
IRDNS2 - reads density file, put current section of map to integer array.
Subroutine to write does not open file and you have to control content
of common block/COMWRF/ ( subroutines C_CR_WR,SET_TITLE) and to use
subroutine: OWFILE before.
WDENS - write current section of map to file
4. Subroutines to read/write coordinate files:
This subroutines uses common blocks: /CRDINF/,/CRD2INF/,/CRD3INF/,
/CRDATM/,/CRD2ATM/,/CRD3ATM/ for read/write title of file and coordinates.
Some subroutines to control the content this common blocks:
C_CR_AT - copy information from common/CRYSTL/ to common/CRDINF/
C_AT_CR - copy information from common/CRDINF/ to common/CRYSTL/
also using CELL parameters from common/CRYSTL/ calculates
reciprocal cell parameters, volume and calc matrix
FRTOCR and CRTOFR
C_CR2_AT - copy information from common/CRYSTL/ to common/CRD2INF/
C_AT_CR2 - copy information from common/CRD2INF/ to common/CRYSTL/
also using CELL parameters from common/CRYSTL/ calculates
reciprocal cell parameters, volume and calc matrix
FRTOCR and CRTOFR
C_CR3_AT - copy information from common/CRYSTL/ to common/CRD3INF/
C_AT_CR3 - copy information from common/CRD3INF/ to common/CRYSTL/
also using CELL parameters from common/CRYSTL/ calculates
reciprocal cell parameters, volume and calc matrix
FRTOCR and CRTOFR
read/write subroutines:
ORCRD - 1. open file for read.
2. reads title of file to common/CRDINF/
RDCRD - reads coordinates to common/CRDATM/
ORCRD2 - 1. open file for read.
2. reads title of file to common/CRD2INF/
RDCRD2 - reads coordinates to common/CRD2ATM/
ORCRD3 - 1. open file for read.
2. reads title of file to common/CRD3INF/
RDCRD3 - reads coordinates to common/CRD3ATM/
OWCRD - 1. open file for write.
2. writes title from common/CRDINF/ to file
WRCRD - writes coordinates from common/CRDATM/ to file.
OWCRD2 - 1. open file for write.
2. writes title from common/CRD2INF/ to file
WRCRD2 - writes coordinates from common/CRD2ATM/ to file.
5. Easy way to understand how to use BLANC subroutines is to look at
the example-programs in "blanc/prog" directory:
read_sf.f - read/write structure factor files
read_dns.f - read/write density files
read_crd.f - read/write coordinate files
reaf_atoms.f - read/write coordinate files and keep all atoms in memory.
Programs use include files from "blanc/for" directory:
nsym-max.fh
atom-com.fh
There are four programs:
1) MTZ2CIF which reads MTZ file and writes output
CIFile. Use program TOBLANC to convert CIFile to BLANC file.
2) DNS2CCP4 which converts density map( BLANC format) to CCP4 format.
3) BLANC2MTZ writes a contents of internal BLANC files:
Fobs, Fcalc, Phases to new MTZ file.
4) CCP42DNS convert CCP4 density map to BLANC density map
You can find these programs in directory: blanc/ccp4
For compilation
1.define compiler setenv BLANC_FORT ...
2. give command: ccp4.setup
Size of any programs easy to change because only one or two parameters
control it. You can find its in the begining of program.
Any program uses include file 'blanc/for/nsym-max.fh':
C -------------------------------------------------------
C --- IPRSYM - maximal number of symmetry operators
C
PARAMETER ( IPRSYM=48 )
C -------------------------------------------------------
If you want you can change it by hand before make setup.