B L A N C 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. The package has been ported to all the major platforms such as Unix, VMS and DOS. ================================================================ Authors: A.A.Vagin, G.N.Murshudov, B.V.Strokopytov 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 ================================================================ HOW TO GET BLANC a) Copy file blanc.tar.gz from ftp site: ftp.yorvic.york.ac.uk ( user: anonymous cd pub/alexei ) 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/unix, start/linux subdirectories and files: sfcheck.tar.gz, molrep.tar.gz, makecif.tar.gz, contact.tar.gz, mir.tar.gz, README b) Compilation. 1. go to directory: blanc/start/unix 2. sh setup.unx or if you want to have CCP4 version of programs give command: sh setup_ccp4 For Linux system: 1. go to directory: blanc/start/linux 2. sh setup.unx 3. if you want to have CCP4 version for programs give command: sh setup_ccp4 --------------------- before running Get commands: 1. "setenv BLANC path_name". Example: "setenv BLANC ~alexei/blanc or put it to your ".personal-cshrc" 2. set path to executable files Example: "set path=($path ~alexei/blanc/exe)" -------------------------------------------------------------------- For details look at BLANC manual in the file: blanc/doc/blanc_descr.txt -------------------------------------------------------------------- Some superprogram have independent from BLANC versions. SFCHECK - pub/alexei/sfcheck.tar.gz MOLREP - pub/alexei/molrep.tar.gz CONTACT - pub/alexei/contact.tar.gz LIBCHECK ! MAKECIF !- pub/alexei/makecif.tar.gz MODCHECK ! EMIN ! MIR ! MIR_II !- pub/alexei/mir.tar.gz TRAHALO ! About these programs see below and also README files in these tar files. --------------------------------------------------------------------- Connection with CCP4. 1. There are two programs: A) MTZ2CIF which reads MTZ file and writes output CIFile. Use program TOBLANC to convert CIFile to BLANC file. B) DNS2CCP4 which converts density map( BLANC format) to CCP4 format. You can find MTZ2CIF,DNS2CCP4 and makefile in directory: blanc/ccp4 For compilation give command: make mtz2cif or/and make dns2ccp4 2. You can have CCP4 version SFCHECK which can read MTZ file. For compilation go to directory: blanc/sfcheck/src and give command: make ccp4. Name of program will be the same as for ordinary version: sfcheck 3. You can have CCP4 version MOLREP which can read MTZ file. For compilation go to directory: blanc/molrep/src and give command: make ccp4. Name of program will be the same as for ordinary version: molrep 4. You can have CCP4 version MIR which can read MTZ file. For compilation go to directory: blanc/mir/src and give command: make mir_ccp4. Name of program will be : mir 5. This possibility uses CCP4 libraries. You must define the path to this libraries by variable CLIB. Give command: setenv CLIB 6. Batch file blanc/start/unix/setup_ccp4 prepares CCP4 version all these programs: SFCHECK,MOLREP,MIR,MTZ2CIF,DNS2CCP4. Go to directory: blanc/start/unix and give command: sh setup_ccp4 --------------------------------------------------------------------- ====================================================================== Independent superprograms: --------------------- MOLREP - is an automated program for molecular replacement * a full-symmetry translation and Packing function. * an automated choice of search parameters. * scaling by Patterson origin peaks. * soft low resolution cut-off. * anisotropic correction of data. * rigid body refinement. * allows input of a priori knowledge of similarity and completeness of the model. * can use second fixed model with correct position and orientation. * can check several peaks of rotation function by computing each translation function and select result by correlation * coefficient. * if the number of monomers is known MOLREP can position the input number of monomers in a simple run. * can check and manage pseudo-translation. * can improve the model before to use. * can use MTZ file. * can compute only Cross rotation or only Translation function. * can compute Self Rotation Function with PostScript plots. * Spherically averaged phased translation function. * Phased Rotation and Phased Translation functions. * fitting two models. --------------------- MIR There are three super_programs for Isomorphous replacement method: MIR, MIR_II, TRAHALO. Main program is MIR. Others may be used for semi-automated solution or if you like to play with parameters of program. 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/ Other prorams are the auxiliary programs. Their input files have BLANC format. You can have these files after program MIR. 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. / --------------------- MAKECIF - 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"/ 4. with Van-der-Waals and H_bond restraints: standard values of distanceis and its actual values in the structure. /file extension "vdw"/ Program can read additional library of monomers. Program rebuilds missing atoms used information from monomer's library. 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. Program can generate hydrogen atoms. MODCHECK - reads CIFiles of coordinates and restraints, gives information about restraints (to DOC_file), writes PDB_file or/and CIFile of coordinates. LIBCHECK - reads library of monomers, 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. Program can generate hydrogen atoms. EMIN performs 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 --------------------- SFCHECK - A program for assessing the agreement between the atomic model and X-ray data. The program requires one or two input files, with the coordinates of the model (in PDB or CIF or BLANC format) and structure factors (in CIF or PDB or BLANC format), and runs completely automatically. 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. For output information program generates PostScript file. --------------------- CONTACT computes inter or/and intra molecular contacts; * can compute contacts only for special atoms ( for example for potential H-bonds); * can generate additional symmetry related atoms (with occupancy = 0) which are closed to initial molecule; can do it only for water molecules (water structure); * checks atoms in special positions and changes multiplicity for these atoms. --------------------- ======================================================================