This data was generated using a version of MolProbity 4.02 (non-cctbx version) modified to run on HTCondor with DAGMan at the BMRB.
This version of MolProbity runs the following programs:

Java (cmd line): java version "1.7.0_111"
Prekin: PREKIN version 6.57, Linux, dated: 130508  NOGUI
Reduce: reduce: version 3.24 07/24/2013, Copyright 1997-2013, J. Michael Word
Probe: probe.2.16.130520
CondorVersion: 8.2.10 Oct 21 2015 BuildID: 345812

These results contain output from MolProbity run in three different ways.  
1) MolProbity was run on the original files.  Note that for these results, clashscores will be invalid for any files without hydrogens.
2) MolProbity was run with reduce -trim and reduce -build.  This removes preexisting hydrogens and readds them, applying Asn/Gln/His flip corrections.
3) MolProbity was run with reduce -trim and reduce -build.  This removes preexisting hydrogens and readds them, not applying Asn/Gln/His flips.

Directory structure on the BMRB FTP site:
oneline_files       - these files contain one line of summary statistics for models in each PDB.
 -> combined/       - combines results from "nmr" and "not_nmr"
 -> everything.zip  - contains all the oneline results
 -> nmr/            - results from NMR PDBs.  Reduce/Probe were run using -nuclear hydrogen bond lengths.
 -> not_nmr/        - results from non-NMR PDBs.  Reduce/Probe were run using -ecloud hydrogen bond lengths.
residue_files       - these files contain one line of statistics for residues in each PDB.  Within each subdirectory, the results from each PDB are separated into different directories by the middle two letters of the four letter PDB code.  So as an example, 1ubq would be located in the "ub/" directory.
 -> combined/       - combines results from "nmr" and "not_nmr"
 -> everything.zip  - contains all the residue results in one directory
 -> nmr/            - results from NMR PDBs.  Reduce/Probe were run using -nuclear hydrogen bond lengths.
 -> not_nmr/        - results from non-NMR PDBs.  Reduce/Probe were run using -ecloud hydrogen bond lengths.

Citations:

MolProbity:
Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21.
and/or
Davis et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Research 35:W375-W383.

HTCondor:
Douglas Thain, Todd Tannenbaum, and Miron Livny, "Distributed Computing in Practice: The Condor Experience" Concurrency and Computation: Practice and Experience, Vol. 17, No. 2-4, pages 323-356, February-April, 2005. 
and/or
Peter Couvares, Tevik Kosar, Alain Roy, Jeff Weber and Kent Wenger, "Workflow in Condor", in In Workflows for e-Science, Editors: I.Taylor, E.Deelman, D.Gannon, M.Shields, Springer Press, January 2007 (ISBN: 1-84628-519-4) 

BMRB:
"BioMagResBank", Eldon L. Ulrich; Hideo Akutsu; Jurgen F. Doreleijers; Yoko Harano; Yannis E. Ioannidis; Jundong Lin; Miron Livny; Steve Mading; Dimitri Maziuk; Zachary Miller; Eiichi Nakatani; Christopher F. Schulte; David E. Tolmie; R. Kent Wenger; Hongyang Yao; John L. Markley; Nucleic Acids Research 36, D402-D408 (2008) doi: 10.1093/nar/gkm957

Contact vbchen AT bmrb.wisc.edu with questions.


When PDB re-releases entries, the new residue result CSVs are appended to the ZIP archive. Therefore you should select "Replace All" if your Zip utility prompts you about overwriting files. Otherwise you will be left with the CSV for the original PDB file and not the remediated one.
[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory  -  
[TXT]README.txt2020-12-04 07:08 3.5K 
[DIR]derived_data/2020-10-05 16:14 -  
[DIR]residue_files/2020-01-07 13:58 -  
[DIR]pdb_files/2016-10-20 12:19 -  
[DIR]oneline_files/2016-10-18 12:02 -  
This data was generated using a version of MolProbity 4.02 (non-cctbx version) modified to run on HTCondor with DAGMan at the BMRB.
This version of MolProbity runs the following programs:

Java (cmd line): java version "1.7.0_111"
Prekin: PREKIN version 6.57, Linux, dated: 130508  NOGUI
Reduce: reduce: version 3.24 07/24/2013, Copyright 1997-2013, J. Michael Word
Probe: probe.2.16.130520
CondorVersion: 8.2.10 Oct 21 2015 BuildID: 345812

These results contain output from MolProbity run in three different ways.  
1) MolProbity was run on the original files.  Note that for these results, clashscores will be invalid for any files without hydrogens.
2) MolProbity was run with reduce -trim and reduce -build.  This removes preexisting hydrogens and readds them, applying Asn/Gln/His flip corrections.
3) MolProbity was run with reduce -trim and reduce -build.  This removes preexisting hydrogens and readds them, not applying Asn/Gln/His flips.

Directory structure on the BMRB FTP site:
oneline_files       - these files contain one line of summary statistics for models in each PDB.
 -> combined/       - combines results from "nmr" and "not_nmr"
 -> everything.zip  - contains all the oneline results
 -> nmr/            - results from NMR PDBs.  Reduce/Probe were run using -nuclear hydrogen bond lengths.
 -> not_nmr/        - results from non-NMR PDBs.  Reduce/Probe were run using -ecloud hydrogen bond lengths.
residue_files       - these files contain one line of statistics for residues in each PDB.  Within each subdirectory, the results from each PDB are separated into different directories by the middle two letters of the four letter PDB code.  So as an example, 1ubq would be located in the "ub/" directory.
 -> combined/       - combines results from "nmr" and "not_nmr"
 -> everything.zip  - contains all the residue results in one directory
 -> nmr/            - results from NMR PDBs.  Reduce/Probe were run using -nuclear hydrogen bond lengths.
 -> not_nmr/        - results from non-NMR PDBs.  Reduce/Probe were run using -ecloud hydrogen bond lengths.

Citations:

MolProbity:
Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21.
and/or
Davis et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Research 35:W375-W383.

HTCondor:
Douglas Thain, Todd Tannenbaum, and Miron Livny, "Distributed Computing in Practice: The Condor Experience" Concurrency and Computation: Practice and Experience, Vol. 17, No. 2-4, pages 323-356, February-April, 2005. 
and/or
Peter Couvares, Tevik Kosar, Alain Roy, Jeff Weber and Kent Wenger, "Workflow in Condor", in In Workflows for e-Science, Editors: I.Taylor, E.Deelman, D.Gannon, M.Shields, Springer Press, January 2007 (ISBN: 1-84628-519-4) 

BMRB:
"BioMagResBank", Eldon L. Ulrich; Hideo Akutsu; Jurgen F. Doreleijers; Yoko Harano; Yannis E. Ioannidis; Jundong Lin; Miron Livny; Steve Mading; Dimitri Maziuk; Zachary Miller; Eiichi Nakatani; Christopher F. Schulte; David E. Tolmie; R. Kent Wenger; Hongyang Yao; John L. Markley; Nucleic Acids Research 36, D402-D408 (2008) doi: 10.1093/nar/gkm957

Contact vbchen AT bmrb.wisc.edu with questions.


When PDB re-releases entries, the new residue result CSVs are appended to the ZIP archive. Therefore you should select "Replace All" if your Zip utility prompts you about overwriting files. Otherwise you will be left with the CSV for the original PDB file and not the remediated one.