PDB Extract

 

pdb_extract - Latest Release Notes

December 3, 2015: The pdb_extract version V3.21 is now released

The followings are the improvements of this version compared to the previous version:

  • Added functions to check the enumeration list in mmcif_pdbx_v5_next.dic Auto correction if the entered values have space or case problems. If wrong values are entered, error messages and the enumeration list from the dictionary will be given in the pdb_extract.log
  • Added data extracts for some new data reduction software (such as XDS, Aimless) new data items (e.g. _reflns.pdbx_CC_half, _reflns_shell.pdbx_CC_half) are extracted from all the programs (HKL, XDS, Aimless/Scala)
  • Add a new function "extract_table" to help to users generate a Table for crystallographic publication.
  • Added/removed data items to comply with the D&A system requirements.
  • Supports the current versions of all the external programs.
  • Modified code to better identify the entity-ploy groups.
  • Complete parsing the TLS groups from Buster
  • Modified the template file to parse the refinement details.
  • Made other extractions standard (such as the program names, versions,...)
  • Simplified the compilation and installation steps
  • Updated all the documentations.

    August 3, 2011: The pdb_extract version V3.11 is now released

    The improvements of version V3.11 compared to the previous version V3.10 are the following:

  • Modified extraction for REMARK 200 for hybrid methods.
  • For REFMAC, change the default NCS residue range (-10 9999) to what is there in the PDB file.
  • Modified extraction of COMPND/SOURCE in a PDB file.
  • Modified function align_use_seqres (memory problem).
  • Add three new data items:
    • _refine.pdbx_overall_SU_R_free_Cruickshank_DPI
    • _refine.pdbx_overall_SU_R_Blow_DPI
    • _refine.pdbx_overall_SU_R_free_Blow_DPI
  • Removed a potential bug in parsing TLS residue range for BUSTER.
  • Corrected parsing of Buster for cases like { ?|* } ?=chainID
  • Corrected mis-match (PHIC and PHIC_ALL) from mtz to mmcif conversion and makestricter parsing for phic(FC with PHIC).
  • Modified _software.classification.
  • Corrected a potential bugs in chain_seq_info (residue ranges for TLS/NCS)

    July 10, 2010: The pdb_extract version V3.10 is now released

    The improvements of version V3.10 compared to the previous version V3.004 are the following:

  • Supports REFMAC version 5.5 and later
  • Supports multiple MTZ file conversion.
  • Has improved handling of NCS data items, even for cases with incomplete data.
  • For PHENIX (version 1.4 & later), extracts additional items, populates TLS/NCS residue range, and automatically distinguishes between neutron and X-ray diffraction data.
  • Completely parses RMSD for BUSTER-TNT (version 2.8 & later).
  • Extracts TLS residue ranges for BUSTER-TNT (version 2.8 & later).
  • Improved parsing of MLPHARE log files.
  • Automatically detects identity type and assigns DNA (_entity_poly.type) as polydeoxyribonucleotide and RNA (_entity_poly.type) as polyribonucleotide.
  • Populates the complete coordinate file according to the current mmCIF dictionary.
  • Supports data extraction for MOLPROBITY.
  • Provides more descriptive error messages.
  • Has updated contact information (e.g. email address, authors, URL, ...) for all supported programs.
  • Automatically removes unit for temperatures

    Sep 17, 2007: The pdb_extract version V3.004 is now released

    The improvements of version V3.004 compared to the previous version V2.00 are the following:

  • Added support for BP3 (version 1.0) for heavy atom phasing refinement.
  • Added support for X-gen (versions 5.5.5 and 5.8.3) for processing of diffraction data.
  • Added support for COMO (version 1.2) for molecular replacement.
  • Added support for BEAST (version 1.1.1) for molecular replacement.
  • Added support for Xplor-NIH (version 2.13) for NMR structure refinement.)
  • Added the NCS extraction from the log file of program CNS (V1.2)
  • Added statistics extraction from the summary file (in addition to the log file) of the program PHASER (V2.1)
  • Added an option (-sol) in the EXTRACT program to update the Matthew coefficient and solvent constant once given the correct sequence in the template file.
  • Added an option (-chain) to add chain to PDB file if missing.
  • Fixed a bug for data extraction regarding to the anisou record.
  • The data template file now fully corresponds to the ADIT data items.
  • Support for PDB v3.1 nomenclature of atoms and residues.
  • Updated all the Xray program extractions for experiments [MR, SAD, MAD, SIR, SIRAS, MIR, MIRAS, AB_INITIO]
  • Added more error/warning messages in the program.
  • Updated the core mmcif modules to the latest version with the STL feature.
  • Supported crystallographic software lists     TOP
    Software applications supported by pdb_extract are listed in the Table below.
    Category Software Versions References
    Data collection
    integration
    reduction
    scaling
    averaging
    HKL/HKL2000
    SCALEPACK/DENZO
    1.30 , 1.96 , 1.97.9 Otwinowski & Minor (1997)
    D*trek 7.0SSI , 7.11 , 9.2 , 9.7 Pflugrath (1997)
    SCALA (CCP4) CCP4(v4.0 , 5.0 , 5.01, 5.02 , 6.0 , 6.01 , 6.02) Evans (1997)
    XDS/XSCALE Nov. 2005 , June 2006, Dec. 2006 , Mar. 2007 , July 2007 Kabsch
    MOSFLM 6.2.2 , 6.2.3, 6.2.5, 7.0.1 Leslie(1998)
    X-gen 5.5.5 , 5.8.3 Andrew J. Howard
    SAINT V6.35A, V7.03A Bruker (2002)
    3DSCALE/PROSCALE N/A Fu (2005)
    Molecular
    replacement
    CNS/CNX 0.9 , 1.0, 1.1 , 1.2 Brunger et al. (1998)
    XPLOR 3.1 , 3.851 Brunger et al (1998)
    AMORE (CCP4) CCP4(V4.0 , 5.0 , 5.01, 5.02 , 6.0 , 6.01 , 6.02) Navaza (1994)
    MOLREP (CCP4) CCP4(V4.0 , 5.0 , 5.01, 5.02 , 6.0 , 6.01 , 6.02) Vagin & Teplyakov (1997)
    EPMR 2.5 Kissinger et al. (1999)
    PHASER 1.2, 1.3 , 2.0 , 2.1 Read(2001)
    BEAST 1.1.1 Read(2001)
    COMO 1.2 Tong(1996)
    Heavy atom
    phase
    determination
    CNS/CNX 0.9 , 1.0 , 1.1 , 1.2 Brunger et al. (1998)
    XPLOR 3.1 , 3.851 Brunger et al (1998)
    SOLVE 2.0 , 2.01, 2.02, 2.06, 2.08 , 2.09, 2.10, 2.11, 2.13 Terwilliger & Berendzen. (1999)
    MLPHARE (CCP4) CCP4(V4.0 , 5.0 , 5.01, 5.02 , 6.0 , 6.01 , 6.02) CCP4 (1994)
    SHARP/autoSHARP 1.3.x , 1.4.0 , 2.0 , 2.01 , 2.04 , 2.2.0 Fortelle & Bricogne (1997)
    SHELXD/SHELXS 97 Sheldrick (1997)
    PHASES 95 Furey (1997)
    PHASER 2.0 , 2.1 Read(2001)
    SnB 2.0 , 2.1 , 2.2 Weeks & Miller (1999)
    BnP 0.93 , 1.0 , 1.02 , 1.05 Weeks et al. (2002)
    BP3 1.0 Navraj S. Pannu(2003)
    Density
    modification
    CNS/CNX 0.9 , 1.0 , 1.1 , 1.2 Brunger et al. (1998)
    XPLOR 3.1 , 3.851 Brunger et al (1998)
    DM (CCP4) CCP4(v4.0 , 5.0 , 5.01, 5.02 , 6.0 , 6.01 , 6.02) Cowtan (1994)
    SOLOMON (CCP4) CCP4(V4.0 , 5.0 , 5.01, 5.02 , 6.0 , 6.01 , 6.02) Abrahams & Leslie (1996)
    RESOLVE 2.0 , 2.01, 2.02, 2.06, 2.08 , 2.09, 2.10, 2.11, 2.13 Terwilliger (2000)
    SHELXE 97 Sheldrick (1997)
    Structure
    refinement
    CNS/CNX 0.9 , 1.0 , 1.1 , 1.2 Brunger et al. (1998)
    XPLOR 3.1 , 3.851 Brunger et al (1998)
    REFMAC5 (CCP4) CCP4(V4.0 , 5.0 , 5.01, 5.02 , 6.0 , 6.01 , 6.02) Murshudov (1997)
    PHENIX 1.0 , 1.1a , 1.22a , 1.3.1 , 1.3b Adams et al (2002)
    SHELXL 97 Sheldrick (1997)
    TNT 5F Tronrud (1997)
    BUSTER-TNT 1.0.2 G.Bricogne (1993)
    ARP/wARP 5.0 , 6.1.1 , 7.0 Lamzin & Wilson, (1997)
    RESTRAIN (CCP4) 4.6 CCP4 (1994)
    NMR
    structure
    determination
    CNS/CNX 1.1 , 1.2 Brunger et al. (1998)
    XPLOR 3.1 , 3.851 Brunger et al (1998)
    CYANA 2.0 Güntert (1997)
    Xplor-NIH 2.13 G. Marius Clore(2003)
    References     TOP
    1. Z. Otwinowski and W. Minor. (1997). Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods in Enzymology, Volume 276: Macromolecular Crystallography, part A, p.307- 326
    2. Pflugrath JW (1999). The finer things in X-ray diffraction data collection. Acta Cryst. D55 1718-25
    3. Zheng-Qing Fu (2005), Three-dimensional model-free experimental error correction of protein crystal diffraction data with free-R test Acta Cryst. D61 1643-1648
    4. SAINT V6.35A, Bruker Analytical X-Ray Systems, Madison, WI, (2002).
    5. Evens, P. R. (1997). "the Scala" Joint CCP4 and ESF-EACBM Newsletter. 33, 22-24
    6. Kabsch, W. (1993). Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26, 795-800.
    7. Leslie A. G. W. (1998), J. Appl. Cryst. 30, 1036-1040.
    8. Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, N., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., and Warren, G.L. (1998). Crystallography and NMR system (CNS): A new software system for macromolecular structure determination. Acta Cryst. D54, 905-921.
    9. Navaza J. (1994) AMoRe: an Automated Package-- --for Molecular Replacement. Acta Cryst. D50, 157-163.
    10. Vagin A. , Teplyakov A. (1997) , MOLREP: an automated program for molecular replacement. J. Appl. Cryst. 30, 1022-1025.
    11. Charles R. Kissinger, Daniel K. Gehlhaar & David B. Fogel, (1999) Rapid automated molecular replacement by evolutionary search. Acta Cryst. , D55, 484-491
    12. R. J. Read (2001) Pushing the boundaries of molecular replacement with maximum likelihood. Acta Cryst. D57, 1373-1382
    13. Terwilliger, T.C. and J. Berendzen. (1999) Automated MAD and MIR structure solution. Acta Cryst. D55, 849-861.
    14. COLLABORATIVE COMPUTATIONAL PROJECT, NUMBER 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763
    15. E. de La Fortelle & G. Bricogne (1997) Maximum-Likelihood Heavy-Atom Parameter Refinement for the Multiple Isomorphous Replacement and Multiwavelength Anomalous Diffraction Methods. Methods in Enzymology 276 472-494
    16. Furey, W. & Swaminathan, S. (1997), PHASES-95: A Program Package for the Processing and Analysis of Diffraction Data from Macromolecules. Methods in Enzymology, 277, 590-620
    17. Weeks, C.M. & Miller, R. (1999). The design and implementation of SnB v2.0, J. Appl. Cryst.32, 120-124.
    18. Weeks, C.M., Blessing, R.H., Miller, R., Mungee, S., Potter, Rappleye, A., Simith, G.D. Xu, H., Furey, W. (2002), Towards automated protein structure determination: BnP, the SnB-PHASES Interface. Z. Kristallogr. 217, 686-693
    19. Navraj S. Pannu,Airlie J. McCoy, Randy J. Read(2003), Application of the-- --complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing ACTA CRYSTALLOGR.,SECT.D. 59, 1801-1808
    20. Sheldrick G. (1997) The SHELX-97 homepage http://shelx.uni-ac.gwdg.de/SHELX/
    21. K. Cowtan (1994), Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography. 31, p34- 38.
    22. Abrahams J. P. and Leslie A. G. W.(1996). Acta Cryst. D52, 30-42
    23. Terwilliger, T. C. (2000) Maximum likelihood-- --density modification. Acta Cryst. D56, 965-972.
    24. G. Bricogne (1993), Direct Phase-- --Determination by Entropy Maximisation and Likelihood Ranking: Status Report and Perspectives. ACTA CRYSTALLOGR.,SECT.D 49, 37-60
    25. Tronrud, D, E., (1997). The TNT Refinement Package. in Macromolecular Crystallography, Part B, Methods Enzymol. 277, 306-318
    26. Lamzin, V.S. & Wilson, K.S. (1997). Automated refinement for protein crystallography. Methods Enzymol. (Carter, C. & Sweet, B. eds.) 277, 269-305
    27. G.N. Murshudov, A.A.Vagin and E.J.Dodson, (1997) Refinement of Macromolecular Structures by the Maximum-Likelihood Method. Acta Cryst. D53, 240-255.
    28. P.D. Adams, R.W. Grosse-Kunstleve,-- --L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter and T.C. Terwilliger.(2002) PHENIX: building new software for automated crystallographic structure determination. Acta Cryst. D58, 1948-1954
    29. Güntert, P., Mumenthaler, C. & Wüthrich, K. (1997). Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283-298.
    30. C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore (2003), "The Xplor-NIH NMR Molecular Structure Determination Package," J. Magn. Res. 160, 66-74.