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Offline xiangjun

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DSSR release history
« on: October 31, 2013, 11:24:21 am »
As the list is becoming quite long, for easy reference, I have split up the DSSR release notes from the main post "DSSR: Dissecting the Spatial Structure of RNA".

V1.x releases
  • v1.6.8-2017mar28 -- fixed a bug in loop identification in edge cases (as in 4fe5); expanded standard bases to include A5 and A3 etc; fixed the 1-unit shift bug in the concatenated backbone suite string; fixed a bug in chain-specific DBN (as in 5pky); revised base-pair criteria to include C.U4--D.U4 pair in 1zh5; extended criteria for type=X A-minor-like motifs (U49 to U20--A76 in 4fe5); checked for output of non-stacked bases independently of stacked ones (as in 4rts); miscellaneous code/manual refinements.
  • v1.6.7-2017mar14 -- fixed a bug in derived dot-bracket notation (DBN) with pseudoknots in special cases; revised --json to work with --get-hbonds for a full list of all H-bonds (DSSR and SNAP); changed type=O to type=X for eXtended A-minor motifs to avoid confusion with the previously documented type 0; lowered the default angle for splayed-apart dinucleotides from 100 degrees to 85; miscellaneous code/documentation refinements. 
  • v1.6.6-2017feb20 -- extended A-minor motifs to include a miscellaneous type other than I and II; added groove widths to helices/stems and sequential number to nts of the JSON output; updated the user manual.
  • v1.6.5-2017jan22 -- revised detection of pairs and helices/stems in rare cases; miscellaneous minor refinements.
  • v1.6.4-2016nov19 -- refined detection of multiplets; added the characterization of terminal bases of helices/stems in the 'Summary' section; revised Jmol-DSSR web interface.
  • v1.6.3-2016oct19 -- added a new section of splayed-apart dinucleotides and larger units; plus miscellaneous code refinements and minor bug fixes.
  • v1.6.2-2016sept19 -- refined the algorithm for identifying kink-turns (K-turns), among many other internal improvements.
  • v1.6.1-2016aug22 -- added the identification and characterization of i-motifs (e.g., 1a83 and 2n89); refined algorithms for the identification of H-bonds and helices; miscellaneous code refactoring.
  • v1.6.0-2016aug06 -- added the --pair-list option to allow for user customizations of base pairs to be analyzed; added an analysis of the global curvature for each nucleic acid chain; plus various code refinements.

  • v1.5.9-2016jul22 -- further refinements of the algorithm for H-bonding detection.
  • v1.5.8-2016jul09 -- added a 'summary' line for each loop, plus miscellaneous code refinements.
  • v1.5.7-2016jun16 -- refined the algorithm for H-bonding detection in corner cases (such as G-tetrads with poor geometry).
  • v1.5.6-2016jun09 -- revised the summary line of DNA/RNA chains when multiple models are involved; consolidated/extended cartoob-block related functionality; internal code refinements and minor bug fixes.
  • v1.5.5-2016may25 -- added the --view option (and related variants) to reset a structure via the principle moment of inertia, as in rotate_mol of 3DNA. The output orientation is in the most extended form, vertically; --blocview (or --block-view, --cartoon-block-view) option is also accepted to mimic the 3DNA blocview script; simplified the command-line help/examble message, and revised the user manual accordingly.
  • v1.5.4-2016may16 -- significantly refined and extended the --frame option to reorient a structure based on a selected reference frame, including the middle frame of two base-pair frames, as in frame_mol of 3DNA; added output of the suite string in dssr-torsions.txt; minor bug fixed and refinements; updated user manual.
  • v1.5.3-2016apr11 -- derived a set of virtual torsion angles using the phosphorus atoms and base origins (see output file dssr-torsions.txt). This set of P-base virtual torsions was first implemented in analyze -torsion of 3DNA v2.1, released in early 2012. See my blogpost titled "Pseudo-torsions to simplify the representation of DNA/RNA backbone conformation" (dated 2012-04-22) for details. Moreover, functions related to the --block-color option have been refined.
  • v1.5.2-2016apr02 -- added the --block-color option to facilitate flexible color customizations of blocks/edges (e.g. minor groove); expanded the definition of junction loops to include the special case of a kissing loop motif mediated by an isolated canonical pair (e.g., 1ehz); various minor internal refinements.
  • v1.5.1-2016mar11 -- miscellaneous code refinements and function enhancements.
  • v1.5.0-2016feb12 -- removed the obsolete --jmol option since the DSSR-Jmol integration is now better served via JSON; added more styles in the cartoon-block representation.

  • v1.4.9-2016jan25 -- fixed inconsistency in the dot-bracket-notation (dbn) output section regarding chain names with more than 1-char (as for 1vy6 in .cif format) -- thanks to Eugene for reporting the bug; refined .r3d output of base blocks for PyMOL rendering, following feedback from Thomas Holder.
  • v1.4.8-2016jan16 -- refined the definition of extended base-pair names ("~Wobble", "~Hoogsteen", "~rHoogsteen", and "~Shear"); fixed a bug in the identification of G quartets in rare cases.
  • v1.4.7-2016jan06 -- extended definition of base-pair names, with "~Wobble", "~Hoogsteen", "~rHoogsteen", and "~Shear" for corresponding pairs with similar geometry but sequences other than G–U, A+U, A–U, G–A, respectively.
  • v1.4.6-2015dec16 -- refined detection of H-bonds, base-pairs, multiplets, and helices/stems for boundary cases.
  • v1.4.5-2015nov23 -- added the --nar-paper option for rigorously reproducing the results reported in the 2015 DSSR Nucleic Acids Research paper; miscellaneous code refinements.
  • v1.4.4-2015nov18 -- refined detection of base-pairs and multiplets in boundary cases; made the output of base-capping interactions by default (i.e., the --more option is no longer needed to be specified for its output).
  • v1.4.3-2015oct23 -- added detection of metallo-base pairs, such as T-Hg-T (4l24) and C-Ag-C (5ay2) from the work of Kondo et al.
  • v1.4.2-2015oct19 -- revised code for circular DNA or RNA molecules and unconventional glycosidic linkages (such as C1'–C1 for DY).
  • v1.4.1-2015oct12 -- checked for potential erroneous usage of option --symmetry with an NMR ensemble (which leads to DSSR effectively taking the models all together); revised output width of id strings.
  • v1.4.0-2015oct10 -- introduced the --nmr option to facilitate processing of NMR ensembles or trajectories of molecular dynamics simulations; added a new section summarizing structural features per nucleotide. Up to this point, DSSR contains all the fundamental features I have had in mind!

  • v1.3.9-2015oct08 -- simplified diagnostic message, and refactored code.
  • v1.3.8-2015oct02 -- added option --cartoon-block, plus a few minor refinements.
  • v1.3.7-2015oct01 -- added option --symmetry (short form: --symm) to take symmetry-related MODEL/ENDMDL ensemble as a whole. This option is useful for x-ray crystal structures where the asymmetric unit is 'half' of the biological unit (e.g., PDB id: 467d -- x3dna-dssr -i=467d.pdb1 --symm).
  • v1.3.6-2015sep18 -- revised JSON output for better DSSR-Jmol integration (thanks to Dr. Robert Hanson). Specifically, a "metadata" property is introduced to collect miscellaneous information, thus simplifying the top-level name space. Moreover, "ntParams" is renamed "nts" for consistency.
  • v1.3.5-2015sep09 -- bug fixes for edge cases in JSON output, based on tests against all nucleic acid structures in PDB; minor code refactoring. The DSSR JSON output has now reached a stable, useable state.
  • v1.3.4-2015sep06 -- fixed a bug in parsing .cif files as in PDB entry 5aj0 (thanks to Eugene for reporting the issue).
  • v1.3.3-2015sep03 -- added output of reference frames of bases and base-pairs in JSON, exposing more of DSSR's functionality to other third-party tools (e.g., for visualization).
  • v1.3.2-2015sep02 -- introduced a new set of "simple" base-pair (bp) parameters that are more intuitive for non-canonical bps. The simple parameters, including Shear, Stretch, Buckle and Propeller, are for structural description only, not suitable for model rebuilding. The non-planarity bp parameters, Buckle and Propeller in particular, have recently received attention in the RNA structure community. This simple set of bp parameter is provided to make DSSR more readily accessible to X-ray crystallographers or cryo-EM practitioners. The new parameters complement, but not replace, the original six rigid-body bp parameters for rigorous description and exact rebuilding of nucleic acid structures.

    When the --more option is specified, the new parameters are available in the main output file, taking an extra line for each bp. For --non-pair, the inter-base angle and minimum distance between base atoms are also listed. The new additions break backward compatibility of the main output file; use the --nar-paper option to stay with DSSR v1.2, as reported in the NAR article. Better yet, users are strongly encouraged to switch to the JSON output format for better connection with DSSR.

  • v1.3.1-2015aug29 -- revised tag names for the --json output based on feedback from Dr. Wilma Olson; along the line, changed the file name dssr-a2bases.pdb to dssr-atom2bases.pdb to make its meaning more explicit for atom over base capping interactions.
  • v1.3.0-2015aug27 -- added option --json to collect all DSSR-derived structural features in the standard JSON data exchange format. This single JSON file makes DSSR results easily parsable, allowing for its seamless integration with other RNA bioinformatics tools. Plus various other minor refinements.

  • v1.2.9-2015jul25 -- added a new section on Reproducing results published in the DSSR-NAR paper to the 3DNA Forum, and documented corresponding auxiliary options in the User Manual.
  • v1.2.8-2015jun15 -- added a new section titled "Additional options" to the User Manual; refined the algorithm for hydration identification.
  • v1.2.7-2015jun09 -- added documentation of two related options: --prefix to customize the prefix of DSSR auxiliary files, and --cleanup to remove those files; other minor changes.
  • v1.2.6-2015mar28 -- revised the interpretation of DSSR to "Dissecting the Spatial Structure of RNA"; added a new option --loop-isolated-pair to exclude isolated canonical pairs in delineating loops; updated the user manual (now 60 pages).
  • v1.2.5-2015mar19 -- revised the helix/stem detection algorithm for circular DNA/RNA structures.
  • v1.2.4-2015mar03 -- refined the algorithm for assigning dot-bracket notation (dbn) in rare cases, plus miscellaneous minor improvements.
  • v1.2.3-2015feb18 -- improved the identification of multiplets.
  • v1.2.2-2015feb06 -- refined the algorithm for assigning helices, plus several code refactoring and enhancements.
  • v1.2.1-2015feb01 -- added the functionality for the "characterization of H-type pseudoknots"; refined the underlying algorithms for identifying H-bonds and base pairs.
  • v1.2.0-2015jan01 -- numerous code refinements and refactoring; added classification of base-stacking interactions (option --non-pair); introduced the helix index that an isolated canonical pair is part of; included metal coordination bonds that phosphate OP1/OP2 atoms are involved in (option --po4); replaced option --long-idstr with --idstr; made option --nested explicit; added a new section on base stacks.

  • v1.1.10-2014nov04 -- refined the algorithm for identifying multiplets; expanded option --non-pair to include all non-pairing interactions; various minor improvements.
  • v1.1.9-2014oct22 -- refined H-bond identification and significantly fine-tuned base pair classification; updated the user manual.
  • v1.1.8-2014oct09 -- fixed a bug in assigning G+A pairs to Saenger type X (10); further refined algorithms for finding H-bonds and base pairs.
  • v1.1.7-2014sep24 -- added auxiliary files (where available) dssr-bulges.pdb, dssr-iloops.pdb and dssr-junctions.pdb to parallel dssr-hairpins.pdb; further refined the algorithm for H-bond detection; significantly improved the User Manual -- by switching to LaTeX, all the hyperlinks and cross references are active, and the excerpted output listings in the manual are auto-synced with the latest DSSR release via a Ruby script.
  • v1.1.6-2014sep09 -- refined algorithms for detecting H-bonding and base-stacking interactions; removed the 4-line header in .bpseq output; checked for chain breaks in pseudoknot report; various code polishing.
  • v1.1.5-2014aug28 -- added the section of atom-base stacking interactions (as in the case of the phosphate OP2 atom of G57 capping over the uracil ring of PSU55 in tRNA "1ehz"); significantly sped up the --non-pair and --phosphate options; miscellaneous code refinements.
  • v1.1.4-2014aug09 -- added the option --nest to remove pseudo-knots (if any), leaving only nested pairs; added a new section to list modified nucleotides; numerous minor refinements.
  • v1.1.3-2014jun18 -- refined the algorithm for deriving dot-bracket notation (.dbn) in RNA structures with higher-order pseudo knots (thanks to Jan Hajic); added secondary structure output in .bpseq format to parallel .ct and .dbn; miscellaneous code improvements.
  • v1.1.2-2014apr19 -- added the option --torsion360 to output (virtual) torsional angle in the range of [0, 360] instead of the default range [-180, +180], following Cathy Lawson's suggestion; renamed "00-n/a" to "n/a" for unclassified Saenger pairs, plus a few other refinements of the User Manual based on feedback from Pascal Auffinger; revised A-minor separator character from '/' to '|' (i.e., from 'A/G-C' to 'A|G-C') based on communications with Bob Hanson.
  • v1.1.1-2014apr11 -- added the option --get-hbonds to find and output all H-bonds in a structure; renamed file ‘dssr-torsions.dat’ to ‘dssr-torsions.txt’; updated the User Manual (50 pages)
  • v1.1.0-2014apr09 -- denoted unnamed bps as '--' for easy parsing (thanks to feedback from Dr. Robert Hanson); added helical radius info for helices/stems, and made the helical rise parameter explicit (thanks to Dr. Wilma Olson); changed '_pars' to '-pars' in the output file for consistency; upgraded DSSR to v1.1.0-2014apr09 due to format changes.

  • v1.0.6-2014apr04 -- revised the algorithm for detecting kissing loops, plus other minor refinements; updated the User Manual accordingly.
  • v1.0.5-2014mar24 -- removed the --note option which has become redundant with notes in the main output file and the DSSR User Manual; shortened output from the --help option by deleting the 'Summary' section; minor code refinements. Added the overlooked subsection "Orientation of helices/stems" and fixed a few typos and inconsistencies in the User Manual (48 pages).
  • v1.0.4-2014mar19 -- minor updates on notes in the main output file to synchronize with an significantly improved DSSR User Manual (46 pages) based on feedback from Dr. Wilma Olson.
  • v1.0.3-2014mar09 -- various improvements for consistency, and finally and most importantly, the DSSR User Manual (45 pages) is out!
  • v1.0.2-2014feb16 -- numerous minor refinements, mostly as a result of writing up the DSSR User Manual (coming soon!).
  • v1.0.1-2014jan31 -- Refined the algorithm for detecting multiplets [thanks to Eugene]; fixed a bug for handling circular DNA/RNA structures [thanks to Pascal]; plus consistency improvements.
  • v1.0-2014jan25 -- The program is robust and mature enough to warrant a v1.0 release. While DSSR will be continuously refined, top priority will be on bug fixes. Wherever practical, future DSSR v1.x releases will remain backward compatible.

Beta-testing releases

  • beta-r30-on-20140118 -- considerably improved annotation and consistency of the main DSSR output file with help from Dr. Wilma Olson, refined algorithms for detecting internal and junction loops, added output of secondary structures in the connect (.ct) format and the extended DBN notation to allow for multiple molecules or fragments, removed the --break-symbol option. This will be the last beta release, and shortly we will move to DSSR v1.0! Please give it a try and let me know anything you'd like to change!
  • beta-r29-on-20140106 -- significantly improved the algorithms for detecting various loops (hairpin, bulge, internal or junction loops), covering many corner cases. List of nucleotides in loops and single-stranded fragments are now presented consistently. Plus many code refinements.
  • beta-r28-on-20131225 -- fixed a bug for missing 0-by-N type (right-side) bulge (thanks to Eugene).
  • beta-r27-on-20131203 -- added the missing bracket ([) to delineate base-pair parameters in detailed output for helices/stems (thanks to Eugene).
  • beta-r26-on-20131128 -- code refinements and refactoring, plus minor bug fixes. Single-stranded fragments now refer to nucleotides not involved in loops or canonical base-pairs (Watson-Crick and G-U wobble); simplified idstr for the non-standard compliant yet commonly encountered PDB files (mostly from MD simulations) with no chain id specified, from e.g. _.G1 to G1.
  • beta-r25-on-20131119 -- added option --break-symbol to delineate chain breaks in dot-bracket notation; listed terminal single-stranded segments; plus code refinements/refactoring.
  • beta-r24-on-20131030 -- refined code for nucleotide characterization; annotated the Levitt pair.
  • beta-r23-on-20130918 -- bug fixes on U-turn identification and missing base pairs.
  • beta-r22-on-20130910 -- minor bug fixes and code refinements; released the DSSR web-interface.
  • beta-r21-on-20130903 -- fixed a rare bug reported by Pascal, and refined the mmCIF parsing code.
  • beta-r20-on-20130830 -- added option --u-turn to detect UNR- or GNRA-type U-turns, plus numerous code refinements.
  • beta-r19-on-20130819 -- added option --po4 (--phosphate) to list H-bonds involving phosphate groups; removed the segid info from nucleotide id-string by default;  refined code internally and fixed minor bugs.
  • beta-r18-on-20130801 -- added support for the mmCIF format; refined code for parsing the PDB format.
  • beta-r17-on-20130723 -- assigned backbone suite names (in file "dssr-torsion.dat") following Richardson et al. "RNA backbone: consensus all-angle conformers and modular string nomenclature"; numerous code refinements and note revisions.
  • beta-r16-on-20130709 -- classified each dinucleotide step into A-, B- or Z-form conformation; simplified output by default. Users are advised to upgrade to this release.
  • beta-r15-on-20130703 -- added output of base morphology parameters for each identified helix/stem.
  • beta-r14-on-20130626 -- auto-detection of 'canonical' kink-turns (k-turns) and reverse k-turns (see my post "DSSR identifies kink-turns!"); numerous code refinements.
  • beta-r13-on-20130618 -- added the PDB segment identifier (segid) into nucleotide id string; refine the algorithm for finding A-minor motifs.
  • beta-r12-on-20130610 -- delineated the components of bulges, internal loops, and junctions, per user request.
  • beta-r11-on-20130603 -- refined the descriptive note with the help of Dr. Wilma Olson; added the --long-idstr option to explicitly delineate fields of a residue id string for easy machine parsing; added the --pucker option to output the sugar pucker following either Altona & Sundaralingam (1972) or Westhof & Sundaralingam (1983) -- see the post "Two slightly different definitions of sugar pucker".
  • beta-r10-on-20130430 -- added a brief descriptive note and a list of generated files to the main DSSR output; revised the command-line --help with more detailed usage info; improved output format, and refined code. Now DSSR is not only self-contained, but also (at least should be) self-explanatory.
  • beta-r09-on-20130421 -- added a least-squares fitted helical axis for each identified helix/stem; classified the backbone into BI/BII conformations and the sugar into C2'/C3'-endo like (see file 'dssr-torsions.dat'); checked for non-pairing interactions (H-bonds or base stacking) with option '-non-pair'; refined code and revised output format
  • beta-r08-on-20130323 -- refined algorithm for multiplet detection, revised the header section to output the numbers of DNA/RNA chains, nucleotides, waters, and metals
  • beta-r07-on-20130322 -- code refinements, minor bug fixes, and more extensive tests
  • beta-r06-on-20130319 -- fixed the "segmentation fault" bug reported by MarcParisien for PDB entry 2a64; revised -h message
  • beta-r05-on-20130316 -- detection of ribose zippers; revision of help message; code refactoring
  • beta-r04-on-20130314 -- detection of kissing loops; output format revisions, including an explicit listing of all nucleotides involved in hairpin loops; internal bug fixes and refinements
  • beta-r03-on-20130309 -- extensive tests against all RNA/DNA-containing structures in the PDB as of March 2013, bug fixes and refinements
  • beta-r02-on-20130306 -- bug fixes, and internal improvements
  • beta-r01-on-20130303 -- initial release
« Last Edit: March 28, 2017, 12:30:04 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]


Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.