Dodson. University of York, Heslington, York Y0. DD, UK. The programs are from a wide variety of sources but all use agreed standard data file formats. The suite is designed to be flexible, allowing users a number of methods of achieving their aims and so there may be more than one program to cover each function. The package has been ported to all the major platforms under both Unix and VMS and is freely distributed to academics by anonymous FTP from Daresbury Laboratory. It is widely used throughout the world. Secondly the Project has a responsibility to provide support, both in installing, documenting and maintaining the suite, and in educating budding crystallographers in methodological and computing techniques. CCP4 / program suite / X- ray / macromolecular crystallography 1 Introduction. CCP4 (Collaborative Computational Project, number 4 - see CCP4 (1. In the 1. 96. 0s macromolecular X- ray crystallography in Britain was concentrated at the Laboratory of Molecular Biology in Cambridge, and the Biophysics Department in Oxford, and the program developers had been members of large groups where ideas were debated and tested on a variety of problems, and there was good computing support. By 1. 97. 9 the number of institutions doing macromolecular structure determination had increased, and the size of the new groups was often much smaller. This new community needed some structured approach to help maintain and extend an adequate set of software, to discuss installation problems, new algorithms and bug fixes, and to educate students in the field. The project started in the UK, modestly funded by the Science and Engineering Research Council (SERC). Now its funding, currently from the Biotechnology and Biological Sciences Research Council (BBSRC) with contributions from industrial companies, has grown to allow the employment of three people based at Daresbury, and to cover post doctoral positions and short term contracts for individuals who are interested in tackling specific perceived problems. Collaboration on the development of the suite was previously extended into Europe under the auspices of the European Science Foundation (ESF) Network of the European Association of the Crystallography of Biological Macromolecules (EACBM). Support. The initial impetus to set up CCP4 was the panic a group of us felt when we realised how alone one was as the only computing enthusiast in a small group, with the biochemists wanting their structure NOW, and infuriated by the failure of the software to deliver. The initial project provided funds to allow the programmers from all the UK groups to meet every three months, and to run an annual two day meeting to address some specific issue. The quarterly meetings allowed members to discuss future developments, to analyse bugs, and to keep in touch in pre Email days. The annual meetings have become valuable both for their information content, for the opportunity they give for members from different laboratories to meet, and for the published proceedings, which are often one of the most up- to- date texts available on the chosen subject. Some of the meetings held to- date are: (1. Refinement of protein structures. DL/SCI/R1. 6 (1. Molecular replacement. DL/SCI/R2. 3 (1. Computational aspects of protein crystal data analysis. DL/SCI/R2. 5 (1. Improving protein phases. DL/SCI/R2. 6 (1. Molecular simulation and protein crystallography. DL/SCI/R2. 7 (1. Accuracy and reliability of macromolecular crystal structures. DL/SCI/R3. 2 (1. Molecular replacement. DL/SCI/R3. 3 (1. Data Collection and Processing. DL/SCI/R3. 4 (1. From First Map to Final Model. DL/SCI/R3. 5 (1. Making the Most of your Model. DL- CONF- 9. 5- 0. Macromolecular Refinement. Now there is a comprehensive Manual, a simple installation procedure for both Unix and VMS machines is provided, there are man pages, documentation, and example procedures, and an active Bulletin Board to provide help and advice to users, and to stimulate discussion. Philosophy of the CCP4 suite. Unlike many other packages, the CCP4 suite is designed to be loosely organised, so that it is very easy for different developers to add new programs or to modify existing ones without upsetting other parts of the suite. It consists of a set of separate programs which communicate via standard data files, rather than having all operations integrated into one huge program. This is the approach successfully taken by Unix, and now apparently being embraced by some of the large commercial software houses. It has some disadvantages in that tasks often require a script to chain together several programs, e. This means that in some cases information from one program needs to be transferred to the next by hand, and initially the programs were less consistent with each other. In recent years a lot of work has been done to improve the consistency and to simplify the input both by assigning sensible defaults and by using standard keywords for input. Converting a program to use the standard CCP4 file formats is generally straightforward, and the philosophy of the collection has been to be inclusive, so that several programs may be available to do the same task. The components of the whole system are thus a collection of programs using a standard subroutine library to access standard format files, a set of examples scripts and documentation available for both the VMS and Unix operating systems. Most of the programs are written in standard Fortran- currently the obsolete FORTRAN7. Ansi C. Briefly, the suite contains programs covering all aspects of macromolecular crystallography from data processing to analysis of a refined model; for example the reduction and analysis of intensity data, structure solution by isomorphous replacement and molecular replacement, and refinement and analysis of the structure. The CCP 4 suite: programs for protein crystallography Collaborative Computational Project, Number 4, The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and. The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray. The CCP4 Suite: Programs for Protein Crystallography on ResearchGate, the professional network for scientists. The program suite for protein crystallography. There are also many utility programs for converting formats, etc. File formats. Users do not usually require detailed information about the format of reflexion, map and coordinate files since libraries are provided for reading and writing them. Crystallographic and book- keeping information is stored in the headers of reflexion and map files to facilitate their use. The reflection and map file formats are binary. There are two basic reasons for this: Clear text files are substantially larger and consequently take more time to read from disc even if the decoding is relatively cheap and space is not a consideration. The columns of the reflection data records are identified by alphanumeric labels and column type flags held as part of the file header information. The user relates the item names used by the program to the required data columns, identifying them by their labels, by means of assignment statements in the program control data. The programs check to see the associated column type is valid for the program operation, e. Additional crystallographic information (title, cell dimensions, column labels, symmetry information, resolution range, history information and, if necessary, batch titles and orientation data) is contained in header records identified by keywords. Program Label. Type. Description. H, K, LHMiller indices.
M/ISYMBATCHYBPartiality flag and symmetry number Batch number. I SIGIJ QIntensity I. F value for derivative n. DP DPHn. D D Anomalous difference for native data (F+ - F- ). Anomalous difference for derivative n. SIGFP SIGDP SIGFPHn SIGDPHn. Q Q Q Qs. FP (standard deviation) s. DP s. Fn s. DPHn. PHIC PHIBP PCalculated phase. Phase. FOM WTW Wfigure of merit weight. Any publication arising from use of the CCP4 program suite should include the following reference: Collaborative Computational Project, Number 4. HLA, HLB, HLC, HLDAABCD H/L coefficents. Free. R- flag Miscellaneous. I R or Ifree R flag (as flag label) Any attribute you require. Figure 1: MTZ standard program labels and column types. The model for an MTZ file is thus based on two components, one (the header) keyed on keywords such as SYMMETRY, CELL, etc. An example helps to make this clear. A reflection file in the CCP4 examples area contains observations for the dendrotoxin from green mamba (toxd, Skarzynski (1. The file contains the native data plus three derivative data sets, one with anomalous measurements. The derivatives are Hg, I and Au. The labels and column types are: H K L FTOXD3 SIGFTOXD3 ( indices, native F and sd)H H H F Q ( column type flags ) FMM1. SIGFMM1. 1 ( Hg F and sd) F Q ( column type flags ) FI1. SIGFI1. 00 ( I F and sd) F Q ( column type flags ) FAU2. SIGFAU2. 0 ANAU2. SIGANAU2. 0 (Au F, SD, F(+) - F(- ), SD) F Q D Q (column type flags ) The header contains the information: Cell Dimensions : 7. Resolution Range: 3. A Space group = P2. These are used as input to the phasing program (MLPHARE) like this: LABIN FP=FTOXD3 SIGFP=SIGFTOXD3 - FPH1=FAU2. SIGFPH1=SIGFAU2. 0 - DPH1=ANAU2. SIGDPH1=SIGANAU2. FPH2=FMM1. 1 SIGFPH2=SIGFMM1. FPH3=FI1. 00 SIGFPH3=SIGFI1. The output labels required for the MIR phase and its figure of merit could be named like this. Hence, after truncate some reflection data records may be entirely missing from the MTZ file, although the reflection indices lie within the measured resolution range. It is strongly recommended that index sets are made complete within the desired resolution range - a script to do this is provided in $CETC/uniqueify. The MTZ file will then contain records where there are indices but no measured data. Furthermore, a particular reflection may be recorded for the native protein but not for a derivative, and the corresponding combined reflection data record should indicate . Maps. The electron density map is stored in a randomly- accessible binary file as a 3- dimensional array preceded by a header which contains all the information needed to describe it. This includes the extent of the array, and the grid it is calculated on, the axis order, the cell and symmetry, a title and the minimum, maximum and mean density. Maps are structured as a number of sections each containing a (fixed) number of rows and each row contains a (fixed) number of columns. The format is also used for envelope masks and images. Kim Group : : Structural Biology Lab learning. Introduction of protein crystallography. Multiple wavelength Anomalous Diffraction(MAD)Theory and methods of data analysis. Space groups. Anomalous dispersion. Reciprocal cell calculation. Protein crystallography on the webcrystallization Pictorial library. Hampton research. Emerald biostructure. Crystallization database. Guide to crystallization. Practical guide of crystallizationdata. TREKHKL Package. MOSFILM in CCP4. Strategy of processing. Example of Mosflm and SCALAAutoindexing with DENZOHKL manualheavy. Heavy atom databank. Heavy atom library. About Xenon. Procedure of derivativephasing. ARP/w. ARP A system for the refinement of. CCP4 A suite of programs covering all aspects of crystallographic. CHART Automatic Structure Solution. CNS A system for structure determination from crystallographic or. NMR data. PHASES Compute phase angles for diffraction data from macromolecular. SAPI heavy atom search program using direct methods. SHELX A set of programs for direct structure solution and refinement. SHARPSNB dual- space direct- methods procedure for determining crystal structures. X- ray diffraction data. SOLVE An automated system for phase determination from MIR and MAD. TNT Xtal. View An interactive system for building and manipulating models. MIR or MAD. data. USF software O related softwares in Uppsala Software Factorymodeling. ARP/w. ARP An automatic model building program. MAINAn interactively driven suite of programs for molecular modeling. OAn interactive system for building and manipulating models in electron. Xtal. View An interactive system for building and manipulating models. Hi. CUP. Ligand databaseprodrg. Ligand drawingmolecular. MR tutorial from data to density. Amore in CCP4. BEAST in CCP4. EPMRMOLREP in CCP4. Queen of Spade. GLRFMRXpicture. Alscript sequence alignment and drawing. Bio. Editor A tool for creating and viewing dynamic, formatted structure. Windows. Bobscript. DINO 3. D visualization program for structural biology data. GRASPProtein. Scope Free viewer to display and manipulate PDB files and create. Pymol. Rasmol. Molmol. Molray. Molscript. Raster 3. DRibbons A program for molecular illustration and error analysis SPOCKVMD Visual Molecular Dynamics. Chimera. MSMS a molecular surface computation. MEAD Macroscopic Electrostatics with Atomic Detailstructure. Biotech Validation Suite. ERRAT Structure Submission Page. PROCHECKVerify. 3D Structure Evaluation Server.
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