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pdb_extract - Latest Release Notes

November 1, 2022: The pdb_extract version V4.0 is now released

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

  • Re-design under python framework
  • Remove dependency on outdated PDB-to-CIF converter by incorporating the converter utilized by wwPDB OneDep system
  • Improve mmCIF format checking on format and dictionary compliance
  • Collaborate with PDBj to use mmCIF editor for author's template file to ensure future compliance
  • Clean up dependencies on old refinement software packages
  • Simplify the features to support modern refinement and data processing packages only
  • Structure Factor file conversion is no longer supported in the standalone package. Please use SF-convert to process structure factor file locally

    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:
  • 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.

     

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