Release note

Changes and improvements have been made as follows.

• version 3.1
  • The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
  • The xPSSS expression has been added in order to select a group of atoms.
  • Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
  • The applet can send information about mouse-picked atoms to JavaScript.
• version 3.1.1
  • Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
  • Some problems in 'trace' command have been fixed.
• version 3.1.2
  • eF-site ID has been changed to a new format.
• version 3.1.3
  • Some problems in xps3 atom selection have been fixed.
• version 3.1.4
  • Some problems in finalization process of openGL rendering have been fixed.
• version 3.1.5
  • The output of 'show xps3' command has been modified.
  • Some problems in 'save png/jpeg' command have been fixed.
• version 3.1.6
  • Some problems in loading an empty polygon file have been fixed.
• version 3.1.7
  • Some problems in initialization process of the applet have been fixed.
• version 3.2
  • 'show site' command has been added.
• version 3.3 beta 1
  • Availabe JOGL version is restricted to JSR-231 beta 5 only.
• version 3.3
  • Both the previous JOGL (version 1.1.1) and JSR-231 are available.
  • The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
• version 3.3.1
  • Some problems in reading a pdbMLplus file have been fixed.
• version 3.4
  • PDB format version 3 can be processed.
• version 3.5
  • Discrimination of DNA and RNA linking nucleotides is based on Chemical Component Dictionary for PDB format version 3.
  • The default representation of the cartoon model has been changed. Commands 'set cartoon_loop_tube', 'set cartoon_round' and 'set ribbonback' have been added.
  • The default parameters of lighting have been changed. Commands 'set ambient', 'set diffuse1', 'set diffuse1_direction', 'set diffuse2' and 'set diffuse1_direction' have been added.
  • Commands 'set pdbml_noatom_url', 'set pdbml_extatom_url', 'set pdbml_plus_url', 'set efsite_url', 'set ext_site_url', 'show pdbml_url', 'show efsite_url' and 'show ext_site_url' have been added.
  • The command-line option '-stdin' has been added to receive commands from stdin stream.
• version 3.6
  • Users can specify the JavaScript function name used in Applet-to-JavaScript Communication.
  • Applet parameter 'file_load_message' has been added.
• version 3.6.1
  • Predefined set of residues has been modified.
  • Old JOGL API is not supported.
• version 3.6.2
  • Latest version of PDBML can be processed.
  • Some problems in mouse control on Mac have been fixed.
• version 3.6.3
  • Molecule file parsing has been modified to detect chain breaks properly by reading the 'label_asym_id' column in PDBML and the TER line in PDB flat file, respectively.
• version 3.6.4
  • Some problems in GUI menu on Mac have been fixed.
• version 3.6.5
  • The jV applet can invoke a JavaScript function when it started.
• version 3.7
  • Commands 'pdbj_describe' and 'pdbj_execute' have been added.
  • Keyword 'xps3' have been replaced by 'pdbj'.
• version 3.7.1
  • Default PDBML URLs have been changed.
• version 3.7.2
  • Some problems in creating png/jpeg image files have been fixed.
• version 3.8
  • Command 'displayatom' has been added.
  • The signed jV applet can save PNG/JPEG image files.
• version 3.8.1
  • In commands 'cartoon', 'ribbons' and 'trace', a backbone will be drawn instead when a chain does not have enough atoms to draw those models.
  • Recognition of amino acids is based on Chemical Component Dictionary.
• version 3.8.2
  • Command 'ball_and_stick' has been added.
• version 3.8.3
  • Binary distribution contains the JOGL library and pre-installation of JOGL is not necessary to use jV.
• version 4.0
  • The program supports PDB format version 4.0.
  • Atom expression has been extended to handle case-sensitive chain ID and label_asym_id in PDBML.
• version 4.1
  • The program runs with new JOGL library (2.0-rc4 or later) which enables jV applets to run on Mac.
  • From this release, the program requires JRE 1.6 or later.
  • Command 'add_backbone' has been added.
  • The program uses MODRES data and chem_comp/type data (PDBML only) to determine residue types.
• version 4.2
  • The program reads polygon CGO (PyMOL-specific Compiled Graphics Objects) files distributed at eF-site system. Command 'load polygon_cgo' has been added.
  • A parameter 'pdbid' and a method 'loadFTP' have been added to applet.
  • When the program loads a PDBML noatom file whose directory is 'all-noatom' or 'XML-noatom', the coordinate file is retrieved from the corresponding directory; '../all-extatom' or '../XML-extatom', respectively.
• version 4.2.1
  • The program runs with new JOGL library (2.0-rc11).
• version 4.3
  • Anaglyph 3D rendering is added to 'stereo' command.
• version 4.3.1
  • A workaround for a cache problem in JRE 1.7 has been added.
• version 4.4
  • The program can read and write mmCIF format files.
  • The program handles biomolecule structures when reading and writing a molecule file.
  • The default setting of PDBMLplus URL has been changed.
• version 4.4.1
  • Some problems in reading mmCIF files have been fixed.
  • The behavior of mouse picking when measuring the distance between two atoms has been changed. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.
• version 4.4.2
  • The program files are signed with a new certificate.
• version 4.4.3
  • Some problems in writing PDB files have been fixed.
• version 4.4.4
  • Some problems in rendering polygons have been fixed.
• version 4.4.5
  • The program shows an error dialog when an input file has no valid data.
  • The program files are signed with an updated certificate.
• version 4.5
  • The program can read and display mmCIF files for small molecules.
• version 4.5.1
  • A file permission problem in writing image files has been fixed.
• version 4.5.2
  • The contact address on the error dialog has been changed.
• version 4.5.3
  • In applet parameters, data files on the same server as the web page can be specified by the path part of URL as well as the full URL.
• version 4.5.4
  • The program files are signed with a new certificate.
• version 4.5.5
  • The program files are signed with a new certificate.
• version 4.5.6
  • The program files are signed with a new certificate.
• version 4.5.7
  • The program files were signed with a new certificate because of the CA certification renewal.
• version 4.5.8
  • PDBML URL to fetch molecule information files has been updated.
  • The applet functionality has been removed.
• version 4.5.9
  • The format of PDBMLplus files has been changed to JSON.
• version 4.5.10
  • Finished providing the signed version and no longer offering the web start version.
  • Default PDBML URLs have been changed.