------------ CCP4 Newsletter - January 1997 ------------
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The BLANC program suite for Protein Crystallography
Alexei A. Vagin¹ ², Garib N. Murshudov¹ ³, Boris V. Strokopytov¹
1. Institute of Crystallography, Leninsky pr.59, Moscow 117333, Russia
2. UCMB-ULB, Free University of Brussels, avenue Paul Heger cp160/16 - P2
1050 Brussels, Belgium
3. Chemistry Department, University of York, Heslington, York, U.K.
Dedicated to the memory of academician B.K.Vainshtein
The BLANC program suite is a set 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 and at the same time allows to build and test new algorithms. Beside a set of small programs, the BLANC system introduces so-called superprograms which represent larger programs composed of several
smaller ones. They utilise 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.
The package has been ported to all the major platforms such as Unix, VMS
and DOS. At the moment a current version of the suite is distributed by
The BLANC program suite project was started in 1979 in the laboratory headed
by B.K.Vainshtein in the Institute of Crystallography, Moscow.
The goal of the project was to develop an independent flexible set of
programs which could communicate with each other through standard data
file formats. The programs can be combined in a many different ways allowing
user to perform any particular task. All computer code is written in
The suite contain programs for analysis and merging of intensity data,
structure solution programs utilising SIR, MIR, SIRAS, MIRAS, molecular
replacement and density modification methods. The complex also contains
programs for crystallographic refinement and the programs for analysis of
the structures. The programs for displaying electron-density, rotation function,
etc. are also available. The suite has been used for the determination of a number of protein structures. Some examples are listed below (Table 1).
Table 1: Examples of protein structures solved using the BLANC suite
| Protein || Reference
| Tyrosine phenol-lyase || Antson et al. 1992
| Catalase || Vainshtein et al. 1981
| Thermitase || Teplyakov et al. 1986
| Ribonuclease C2 || Polyakov et al. 1988
| Ribonuclease Pb1 || Pavlovsky et al. 1988
| Aspartataminotransferase || Malashkevitch et al. 1995
| Pyrophosphatase || Chirgadze et al. 1989
| Dehydrogenase || Lamzin et al. 1992
The program suite
The main idea behind the BLANC suite is simplicity. Special
attention during development of the program system was paid to make it
as user-friendly as possible:
Most of BLANC programs do not require large memory. Most of them can be
run on IBM PC with 640 K memory. All BLANC programs are written in standard
FORTRAN codes and can be running at least by MS-DOS, VMS VAX, UNIX.
Some of the BLANC programs and superprograms are listed in Table 2 and 3.
- All programs demand minimal necessary parameters. Most of them have
- It is possible to use programs in dialogue mode or in batch mode.
Modern computing technology 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-explanatory because
there are short prompts with explanations.
- If necessary it is possible to use keywords to change certain
parameters. Keywords are printed by the programs at the beginning
- Each program has a short description. You can find it in the program
texts or in the BLANC manual.
Table 2: Main BLANC programs
| Program || Function
| A. Entrance and exit.
| readPDB || converts coordinates file formats to CIF
| TOBLANC || converts structure factors to BLANC format
| FROMBL || converts structure factor file into CIF
| writePDB || converts coordinates to PDB file
| B. Fourier transformation.
| COEF || calculates various kinds of Fourier coefficients
| FFT || calculates maps using FFT
| RFT || calculates structure factors
| C. Look up.
| ISOLINE || draws maps 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 coordinate files
| JOINFL || merges the files of structure factors or phases
| SORTMRG || reads, sorts, averages the files of structure factors or phases
| 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
| H. Isomorphous replacement.
| PHASE || calculates Henrickson-Lattman coefficients for a derivative
| REFINE || heavy atom's full matrix refinement
| J. Refinement.
| ROTLSQ || rigid body refinement
| K. Others.
| GENDEN || generates electron density
| PEAKSRCH || map peak search
| WATPEAKS || water peak search and water replacing
| FIT || superimposes two sets of coordinates
| ABCDPH || phases from Hendrickson-Lattman coefficients
| PHABCD || Hendrickson-Lattman coefficients
| HISTOGRM || histogram matching
| SURFACE || solvent accessible surface area
| FRAGSRCH || builds full atomic model of a protein using C_alpha atom coordinates
| CONTACT || computes inter or/and intra molecular contacts
| L. Not converted to current version yet.
| SEQSRCH || searches aminoacid sequence in the local Sequence Data Bank.
| ALIGN || aligns aminoacid sequences
| BBONE || inserts side chains of a protein into electron density map
| PATLSQ || refines orientation of a model before translation function search
| GROUP || converts scattering from protein atoms to group scattering factors
| LOCSCL || anisothermal local scaling
| DPLOT || draws PostScript stereo picture of the model with electron density
| SKELETON || density skeletonisation procedure
Table 3: BLANC superprograms
| Program || Function
| A. Isomorphous replacement method:
| MIR || automated heavy atom search and phasing
| SIR || automated one derivative heavy atom search
| PATTSRCH || automated reciprocal heavy atom structure
| B. Molecular replacement method:
| MOLREP || performs automated molecular replacement search
| SELFROT || calculates self-rotation function
| CROSSROT|| calculates cross-rotation function
| TRFUN || calculates translation and packing function
| C. Refinement:
| MMM || Macro Molecular Minimisation/Crystallographic
| MAKECIF || creates list of geometric and energetic parameters
| LIBCHECK|| reads library of monomers, performs various checks
| EMIN || performs energy minimisation
| DENMOD || phase refinement by density modification
| D. Others:
| OMIT || calculates omit synthesis phases
| OMIT_MAP || creates global omit map
| SFCHECK || checks quality of X-ray structures
BLANC maintains a library of subroutines for performing the basic
crystallographic and programming operations. Common subroutines, e.g.,
to open and close data files, read and write data, FFT, matrix operations,
etc. are gathered in a special library (LIBUTILS). This shortens
markedly program code and makes it easy to read and modify the programs.
Each program has a subroutine version gathered in another library (LIBSUBR).
This allows a programmer to develop larger programs composed of smaller
Three levels of programming in BLANC. Introduction of superprograms
There are three main levels of programming modules in the BLANC
suite of programs. The first level is superprograms. The superprograms normally
implement some method (e.g., molecular replacement using known model). Some
programs may act like subroutines inside superprogram. On the second level
we have usual crystallographic programs which perform basic operations like
calculation of structure factors, electron density etc. They use subroutines
from the library. The subroutines themselves constitute a third level. The main
goal of this programming level is to solve local tasks only: matrix operation,
FFT, opening and closing files, etc.
These special arrangement of BLANC programs simplifies significantly
development of new programs.
Original features of BLANC
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 (to be be published elsewhere), program
for black-box molecular replacement, black-box heavy-atom search and phasing,
global omit map program (Vagin, A.A., unpublished results) and others.
There are four main types of file format for reflection data,
map data, coordinate data and graphics meta-files. The coordinate
data files are in ASCII but reflection and map files are binary.
The BLANC reflection files in most cases uses 12 bytes of disk memory per
reflection. Three reflection indices are packed into one integer*4. Two
real numbers are used for storing information about amplitude and error
The header records contain information such as cell dimensions and
symmetry operators. The reflection data are stored notionally as columns
of real numbers. There is no need to mark columns by special labels since
native, derivative and calculated data are always kept in separate structure
Maps are stored in a binary sequential access files as a three dimensional
array preceded by a suitable header which contains information about map
dimensions, cell, symmetry information, maximum and minimum, mean and
root-mean-square deviation density values, etc. Each density grid point is
packed into two byte integer. There is a possibility to convert BLANC map
format to other map file formats for use on graphical devices.
The standard coordinate file format is close to mmCIF format (Bourne et al.,
program suite allows conversion from BLANC/mmCIF format to the PDB (Bernstein et al., 1977) format
and vice versa.
Graphical programs produce output in PostScript format.
Documentation, Installation and Distribution
The BLANC manual gives the details of installation procedures. In order
to run the programs certain environment variables need to be set to appropriate values.
Output document files are produced which contain necessary information
about the progress of each particular run of the program.
The program suite has been implemented on a large number of hardware
platforms including Unix. Installation is straightforward and full instructions
are given in the BLANC manual.
The BLANC program suite is licensed free to academic institutes. The
programs may be obtained by Internet ftp from firstname.lastname@example.org.
(First read file: pub/alexei/blanc/README). Several programs and
superprograms independent from the BLANC suite (SFCHECK, MOLREP, CONTACT,
MAKECIF, EMIN, LIBCHECK etc.) are kept in separate directories at the
anonymous ftp site. Separate arrangements can be made for commercial
organisations. For further details contact Dr.A.Vagin (email:
We are very grateful to all our former colleagues who made significant
contributions to this project helping us to eliminate bugs in the programs.
We thank them for numerous scientific discussions as well.
- Antson, A.A., Strokopytov, B.V., Murshudov, G.N., Demidkina, T.V.,
Fogelman, H.K., Paskhina, O.G., Hennig, M., Nekrasov, Yu.V., Popov, A.N.,
Rubinsky, S.V., Harutyunyan, E.H. (1992) Three-dimensional structure of
tyrosine phenollyase at 4.5 A resolution Kristallografiya 37,
- Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Mayer, E.F., Brice,
M.D., Rogers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for molecular
J.Mol.Biol. 112, 535-542.
- Bourne, P.E., Berman, H.M., McMahon, B., Watenpaugh, K., Westbrook, J., No.1,
Fitzgerald, P.M.D. "The Macromolecular CIF Dictionary (mmCIF)".(1996) In:
Methods in Enzymology in press
- Chirgadze, N.Yu., Kuranova, I.P., Strokopytov, B.V., Harutyunyan, E.G.,
Hohne, W. (1989). Crystal structure determination of MnP-complex of
neorganic pyrophosphotase from yeast using the molecular replacement
method at 2.7 A resolution. Krystallografiya 34, 1446-1450.
- Lamzin, V.S., Aleshin, A.E., Strokopytov, B.V., Yukhnevich, M.G., Popov,
V.O., Harytyunyan, E.H., Wilson, K.S. (1992). Crystal structure of
NAD-dependent formate dehydrogenase. Eur.J.Biochem. 206, 441-452.
- Malashkevich, V.N., Strokopytov, B.V., Borisov, V.V., Dauter, Z.,
Wilson, K.S. and Torchinsky, Yu.M. (1995). Crystal structure of the closed
form of chicken cytosolic aspatate aminotransferase at 1.9 A resolution.
J.Mol.Biol. 247, 111-124.
- Pavlovsky, A.G., Polyakov, K.M., Borisova, S.N., Strokopytov, B.V.,
Vagin, A.A., Vainshtein, B.K. (1987). Structural bases for nucleotide
recognition by guanil-specific ribonucleases. In: Proceedings of the 6th
International symposium on Metabolism and Enzymology of Nucleic Acids,
(Eds. Zelinka, J., and Balan, J.). Bratislava, 323-330.
- Polyakov, K.M., Strokopytov,B.V., Vagin, A.A., Bezborodova, S.I.,
Orna, L. (1988). Three-dimensional structure of RNase C2 from Aspergillus
clavatus at 1.35 A resolution. In: Proceedings of the 6th International
Symposium on Metabolism and Enzymology of Nucleic Acids (Eds. Zelinka, J.
and Balan, J.). 227-231. Plenum Press, New York - London.
- Teplyakov,A.V., Strokopytov,B.V., Kuranova,I.P., Popov, A.N.,
Harutyunyan, E.H., Vainshtein, B.K., Froemmel, C., Hoehne,W.
(1986). X-ray study of thermitase at 2.5 A resolution.
Kristallografiya 31, 931-936.
- 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, (1989) 24,
- Vainshtein, B.K., Melik-Adamyan, W.R., Barynin,V.V., Vagin, A.A.,
Grebenko, A.I. Three-dimensional structure of the enzyme catalase.,
(1981), Nature 293, p.411-412.
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