Versions of FirstGlance in Jmol

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FirstGlance in Jmol
Version History

December 10, 2006 - January 14, 2007: Version 1.0 (with Jmol applet version 10.2.0).
1. Dec 10: After seven months of service, no major problems came to light in version 0.991, so I deemed it version 1.0 with no further changes.
2. Jan 14: Added What Is FirstGlance in Jmol? (Thanks to Phil Leader for suggesting this.)
3. Jan 14: Added instructions for copying static snapshots of molecular views and pasting them into presentations or documents. Also mentioned MolSlides in Jmol. The new instructions are linked to the bottom of every help panel.
May 10, 2006: Version 0.991 (with Jmol applet version 10.2.0).
1. Non-standard residues are now shown as crosses ("stars" in Jmol command language) by default. The crosses can be hidden in More Views.., or Ligands+. This change was made in accord with the goal of not leaving important information invisible. Crosses were chosen because they don't distract too much from the backbone displays when there are many non-standard residues, as for 1EVV. Examples: 1EVV, 1BKX.
2. New Exit buttons were provided for Hide.. and Center Atom.., replacing the former exit links.
3. At the main page, enabled pressing Enter (in addition to clicking the Submit button) to submit a PDB code to start a FirstGlance session.
4. Fixed a bug that prevented the atom identification report from displaying, to the lower left of the molecule, when the first operation performed in the session was clicking on the molecule.
5. Fixed a bug in atom identification reporting that occurred only in Mac Safari with the latest java update. This bug caused the Safari window to disappear suddenly, at least after a recent java update was released by Apple.
6. Fixed several bugs that prevented the PDB identification code from showing, to the upper left of the molecule, after the background color changed.
7. Minor improvements/corrections in documentation.
May 3, 2006: Version 0.99 (with Jmol applet version 10.2.0).
1. Contacts.. is a new option to show atoms contacting any "target" moiety, which is selected by clicking on the molecule, or with the new Find.. option (see next item). Four views of atoms contacting the target are available, with increasing levels of detail. Distances can be measured between putatively non-covalently bonded atoms. Hydrogen atoms (if present in the model) can be displayed. Seven kinds of non-covalent bonds can be displayed or hidden independently of each other.
2. Find.. is a new option that puts yellow halos around atoms designated by sequence number, 3-letter residue abbreviation, or element name. The halos are visible in all views.
3. A new Snapshot Gallery was provided.
4. More Views.. has a new option to show all salt bridges and cation-pi orbital interactions throughout the molecule.
5. Isolated standard amino acids or nucleotides, invisible in the "backbone" displays of previous versions, are now spacefilled in the initial view, and included in Ligands+ (More..). Selection of these was made possible by a new Jmol command, "connected" (More..).
6. Solutions were implemented to handle hiding or selecting the single unnamed chain in some PDB files, as well as ligands that have chain designations (such as heme in 2HHD). These are important in the new Contacts.. target selection interface, and they improve the function of Hide.. over the previous release.
7. Hide Hydrogen was added to the Hide.. interface. This enables uncluttering ligands or non-standard residues. (Example: 1AL4 has hydrogen on both.)
8. There is a new Reset link that attempts to reset the session to the initial view, and most of the initial settings. I've undoubtedly overlooked some things that need resetting.
9. Gaps in the coordinates, compared to the sequences crystallized, can be located using new documentation, which links to the "SEQRES to Coordinates" alignment (S2C) resource by Wang and Dunbrack.
10. A button for accessing the sequences and gaps help, and the link to S2C (see previous item) was added to the main control panel, next to the PQS, PDB, and OCA buttons.
11. Most links and buttons now display pop-up help when the mouse is held over them for a few seconds.
12. The inability of Jmol to report atom identifications when slab is on has been handled better. Slab is forced off when selection by clicking is needed (Contacts.., Hide..). When Slab is on, the hover and echo identification reports are replaced with a "Sorry..." message.
13. Slab thickness can now be controlled (3 steps).
14. The definition of "carbohydrate" was greatly improved (for the "hide carbohydrate" checkbox). See
15. Rare Anomalous atoms are no longer invisible, but are shown as dots.
16. Hidden atoms are now listed by element, sequence number, and chain, rather than by serial number. (Serial number is used internally.)
17. Specifications for a future interactive sequence listing were developed.
18. Updated many help documents, including and Known Unresolved Issues. Added a section on selection of unnamed chains to Technical Information. A new list of Jmol Bugs and Limitations gathers together information scattered in other FirstGlance documents, and buried in its javascript/Jmol script code.
19. The help for N->C Rainbow now includes a spectral color sequence.
20. Added a "mascot" image to the main page.
21. mmCIF format atomic coordinate files can now be loaded instead of PDB format files, using a new Advanced Option available from the main page. CIF files do not work properly in FirstGlance. CIF loading is provided for testing purposes only. See Preliminary CIF Observations.
22. Bug fixed: The axes, unit cell, and boundbox checkboxes under More Views.. did not work in Gecko browsers in FGiJ 0.98.
March 13, 2006: Version 0.98 (with Jmol applet version 10.00.48).
1. Thanks to PDB files can now be uploaded for display in FirstGlance in Jmol. There is a new option on the main page to do this. for inserting such an upload slot into any web page are provided.
2. Added a new view option Hide.. that hides clicked chains, residues/groups, or atoms; or all protein, DNA, RNA, or carbohydrate. The hidden moieties remain hidden in all views, until explicitly re-displayed.
3. Added a PQS "button" in the control panel (upper left panel, near the PDB and OCA buttons).
4. More Views.. now includes a new section on evaluating model quality, with "color by temperature" (thanks to Gale Rhodes) and a link to MolProbity.
5. More Views.. now includes checkboxes to show the axes, unit cell, or bound box.
6. More Views.. now includes a link for visualizing dipole moments in Jmol.
7. Added 1IGT (antibody) to the Gallery to provide an example with disulfides in multiple chains, and both inter- and intra-chain disulfides.
8. Fixed a bug in Vines.., Hide Sidechains that failed to hide the sidechains in nucleic acids.
9. Korea was added to the list of mirror sites.
10. The advanced option to use browser frames was discontinued.
February 2-12, 2006: Version 0.97 (with Jmol applet version 10.00.48).
1. The PDB code (or filename) is now the first word in the title of the FirstGlance window. This makes it easy to distinguish windows showing molecules from each other, and from the FirstGlance main page window.
2. It is now possible to enter a molecule's URL into a form slot on the main page, to display a molecule from any server (in addition to a PDB identification code).
3. Ligands+ are now shown by default in the initial view. The definition of Ligands+ has been changed to exclude most non-standard amino acids and nucleotides. When the Ligands+ button is depressed, or in More Views.. (new, see below), the accompanying help now includes a checkbox to show non-standard residues. The distinction between Ligands+ and Non-standard residues is sometimes incorrect. Notes were added to explain these definitions, and the examples of the problems were documented.
4. Disulfide bonds are shown by default in the initial view, in all backbone trace views, and in Vines.
5. New entries in the Gallery illustrate disulfide bonds and non-standard residues.
6. Backbones are no longer interrupted by non-standard amino acids and nucleotides. (Formerly, these were displayed as Ligands+, which interrupted the backbones.) For more information, see the new notes on non-standard residues.
7. In the Vines.. display, there are now (in the help panel) new checkboxes to
  1. Hide sidechains.
  2. Display more detail: all non-water atoms as sticks,
  3. Hide hydrogen.
8. In the Ligands+ display, there is now (in the help panel) a new checkbox to display smaller ligands+ atoms.
9. When water is displayed, there is now (in the help panel) a new checkbox to display smaller water atoms.
10. At the time of this release, mouse hover atom identification reports were not working in OSX 10.3.9 (but worked in 10.4 and Windows). Therefore, clicking an atom now identifies it at the lower left of Jmol, and in the browser status line. The report to Jmol required implementing pickCallback(), which may not work in some browsers. A problem remains reporting the element in these reports. The hover report remains, when it works.
11. Using clicking for atom identification required changes in the centering mechanism. The former Center All link was changed to Center Atom. The help accompanying the latter offers a link to Center All.
  - The present implementation was complicated by the need to turn centering off automatically, when some view links or buttons are pressed by the user before centering was turned off. This was implemented.
12. The PDB code shown in Jmol at the upper left now changes automatically to a contrasting color when the background is changed. (Previously, it remained black, becoming invisible on a black background.)
13. Known unresolved issues was revised, and unimplemented plans for future enhancements were added.
14. Several mirror sites are now listed.
15. A new link More Views.. has been added to the upper left control panel. The links to additional viewing options that were formerly in the introductory help have been moved to this new help section, and expanded. New here is information about measuring distances and angles, or opening the Jmol console for entering script commands. In FirstGlance, default units for reporting distances are Ångstroms (Jmol's default is nanometers, rarely used by protein structure scientists).
16. The link to Protein Explorer, formerly in the upper left control panel, has been moved to the More Views.. help section.
17. The term Structure Explorer is no longer in use at pdb.org. The link formerly of that name has been replaced with a PDB graphic.
18. Adjacent to the PDB link, a graphic link to the OCA Browser Atlas entry has been added.
19. Fixed bug that reversed the Charge cationic/anionic colors in the color key. (These colors were never reversed in the molecular view.)
20. Fixed bug that reversed the Solvent and Ligand colors in the Composition view. (Thanks to Frieda Reichsman for pointing out this bug.)
21. Tested dozens of potentially problematic PDB files, documenting the results. See links at the bottom of About FirstGlance.
22. Calcium ions are erroneously deemed "protein" by Jmol (through 10.00.48). Other metals appear to be correctly deemed "hetero" and "ligand" (including at least Fe, K, Mg, Mn, Mo, Na, Zn, Cd). The command scripts of FirstGlance were modified for the special case of calcium, to make it display under "Ligands+". (Implemented Feb 4, 2006).
23. Tried to prevent problematic atoms from remaining invisible (implemented February 4, 2006).
  - Rarely, Jmol fails to deem standard amino acids as protein. Therefore, "protein" was broadened to include the 20 standard amino acids plus atoms deemed "protein" by Jmol, which (usefully) includes hetero atoms for non-standard residues. Examples. Although the backbone trace displays currently (Jmol 10.00.48) fail to connect the alpha carbons of these amino acids, they are shown spacefilled to avoid leaving these parts of chains invisible. An example is 1AL4.
  - Rarely, Jmol fails to assign covalent bonds that should be present. Such groups of atoms are invisible in wireframe (stick) rendering, the normal rendering for the Vines display, which is supposed to show all non-water atoms. Therefore, in Vines, all non-water atoms are shown spacefilled as well as wireframe (or backbone). The diameter of the spacefill is the same as the wireframe (or backbone); hence, when bonded, the spacefilled atoms are hidden within sticks (or backbone). When not bonded, they are visible as small spheres. Examples with many inappropriately non-bonded atoms are 1AL4 and 2SOC.
24. Added additional information at the bottom of Technical Information for Developers.
25. Added a free visit counter, kindly hosted by sitemeter.com. Clicking on the count (below "Please be patient" when the application starts) reveals referring sites, a world map showing locations of visitors, and browsers and platforms used by visitors, among other useful information.
November 26, 2005: Version 0.96 (with Jmol applet version 10.00.43). Changed permanent URL to firstglance.jmol.org. Provided downloadable source code for server installation or application enhancement by developers, along with new documents on installation and PDB data file access methods. Added new document Known Unresolved Issues. Fixed bug that made the Technical Gallery fail to obey advanced options.
November 19, 2005: Version 0.95. Redirected to molvis.sdsc.edu for consistently fast speed of applet and PDB file download. Implemented mechanism for loading PDB files from arbitrary URL's. Separated server configuration variables into file config.js. Completed most documentation. Much polishing.
October 10, 2005: Redirected delivery from bioinformatics.org to firstglance.bioinformatics.org (a different physical server) to improve speed of applet download.
October 3, 2005: Version 0.9. Able to load from PDB Id's, and bundled PDB files (2 in localPDBFiles), but not from an arbitrary URL.

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