Versions of FirstGlance in Jmol

FirstGlance in Jmol
Version History

January 3, 2016: Version 2.4 with JSmol/signed Jmol version 14.4.1 update 2015.12.23.
Version 2.4 provides updates and bug fixes, especially related to ConSurf.
1. Clicking on an atom now reports the chemical element in addition to the atom ID. The element was previously reported in the hover message.
2. When slab is on, dragging at the right edge of Jmol no longer moves the slab plane. It has been restored to zooming as usual. A new gesture, Alt+Shift+drag up/down, now moves the entire slab towards or away from the viewer.
3. The help for the water toggle button now adds "Protein crystals are highly hydrated, ranging from about 30% to 70% water in different crystals." The More.. link there provides literature citations.
4. Triple clicking seems to be needed for distance/angle measurements (only when using Java). The Tools tab Distances/Angles help now mentions this.
5. The documentation for one-letter codes for amino acids is more detailed and a reference is cited.
  
  Updated:
6. The most popular browsers have been re-tested in Windows 7, XP, and OS X, and browser compatibility information has been updated. Notably, Google Chrome no longer supports Java, and the new Edge browser in Windows 10 does not support Java. Also, a change in Chrome 47, December 2015, caused JSmol to be unable to rotate molecules until Bob Hanson made a compensating change in JSmol. Finally, the Maxthon browser has been included. All tested browsers can now be spoofed. Spoofing simply causes FirstGlance to show the relevant recommendations -- it does not cause the browser being used to emulate another browser.
  - Spoof Chrome*
  - Spoof Edge
  - Spoof Firefox
  - Spoof Internet Explorer
  - Spoof Maxthon (JSmol recommendations are more urgent in Windows)*
  - Spoof Opera*
  - Spoof Safari
  * Recommendations are more urgent when the molecule has >10,000 atoms, e.g. 7ahl.
7. The visitor counter had been courtesy Sitemeter.Com since February 8, 2006, recording 583,670 visitors (approximately 1.3 million page views). Due to problems with Sitemeter, the counter was changed to StatCounter.Com, setting the initial count to the final Sitemeter count. This change was made online in the previously released FirstGlance 2.32 on November 12, 2015.
  
  ConSurf related Bugs fixed:
8. The Backbone, Cartoon and Spacefill buttons in the ConSurf control panel did not restore ConSurf colors after they were changed in the FirstGlance control panel.
9. The Backbone, Cartoon and Spacefill buttons in the ConSurf control panel did not hide water that may have been displayed in the FirstGlance control panel.
10. The Backbone and Cartoon buttons in the ConSurf control panel did not turn off all renderings that might have been used in the FirstGlance control panel (e.g. secondary structure rockets or traces).
11. The Reset button in the ConSurf control panel did not restore the gray color of backbones of chains not colored by evolutionary conservation.
12. The 4 views were displaying unwanted water due to remediation in the Protein Data Bank which assigned chain names to water.
13. ConSurf was reporting sequence identity between some non-identical chains (e.g. chains A and P in 2vaa).
14. When Sequence Numbers or Residue Names were checked, in most Views, they were colored by chain rather than by the color scheme of the View (e.g. N->C Rainbow).
15. The ConSurf Colors checkbox was inappropriately greyed out for some Views (e.g. Thin Backbone).
16. The ConSurf Colors checkbox was inappropriately greyed out when Sequence Numbers or Residue Names checkboxes were used.
17. The Isolate tool in the FirstGlance control panel was turning off ConSurf coloring.
18. Dots in view 3 remained yellow after view 2.
19. Toggling the Spin, Background or Quality buttons in the ConSurf control panel did not propagate those button states to the Molecule Information Tab or the Tools Tab in the FirstGlance Control Panel.
20. Dots were not being shown around the balls and sticks of ligands.
  
  Other Bugs fixed:
21. With certain large molecules (for example, 7ahl), in JSmol, Firefox would freeze for about one minute when the first operation was requested in FirstGlance (for example, toggle spinning off). Thanks to Bob Hanson for fixing this bug in JSmol!
22. Center visible moieties in the Hide.. dialog was broken in FirstGlance version 2.2.
October 19, 2015: Version 2.32 with signed Jmol/JSmol version 14.4.0 update October 17, 2015.
1. Browser compatibility and performance with Jmol has been updated, and now includes Microsoft Edge, a browser first released in Windows 10.
2. Browser advice: Advice on which browser to use has been updated to handle the Edge browser. Recommendations appear in yellow banners, and can be seen, without installing multiple browsers, by spoofing a particular browser:
  Bugs fixed:
3. The certificate for the Jmol Java applet was inadvertantly revoked on October 15, 2015, causing operation of all earlier versions to be denied.
4. In JSmol (HTML5, no Java) the JSmol menu could not be opened by clicking on the frank or right-clicking in JSmol. This longstanding bug has been fixed thanks to Bob Hanson.
5. In the help for Sequences, the links to Uniprot sequences stopped going directly to the sequences section (due to a change at Uniprot).
September 5, 2015: Version 2.31 with signed Jmol/JSmol version 14.3.7_2014.09.20.
1. The Google Chrome browser stopped supporting Java on September 1, 2015. This release of FirstGlance intercepts a request to use Java in Chrome, suggesting that you use a different browser (Internet Explorer, Firefox and Safari all support Java), or use FirstGlance without Java.
June 16, 2015: Version 2.3 with signed Jmol/JSmol version 14.3.7_2014.09.20.
1. Sequence numbers and residue names can now be displayed for all residues. New checkboxes are located at the bottoms of the Molecule Information Tab, Views Tab, and Tools Tab, just below the Labels (S-, X, ?) checkboxes.
2. An index to all the capabilities of FirstGlance, and where to find them, has been created: Where? How? is linked at the bottom of every tab except Preferences, and underneath the molecule.
3. A new Practical Guide to Homology Modeling, which also tells how to find X-ray or NMR models, is now linked to the first page at FirstGlance.Jmol.Org, and in the Resources tab.
  
  Bugs fixed:
4. Putting halos on some atoms (with Find..) caused the automatic centering to fail when using Isolate...
5. Under Sequences (Molecule Information Tab) the link to PDBe (Europe) has been removed. The PDBe website was restructured and the interactive sequence display seems no longer to be available.
6. Reset was not resetting the Labels checkboxes (bottom of every tab except Preferences).
7. Crystal Contacts (Tools tab) was not showing any balls for contacting nucleotides that lacked a phosphorus atom (5' terminal nucleotides). The c5' atoms of those nucleotides are now shown as balls. For example, 14 nucleotides contact the asymmetric unit of 1d66. 12 of those have phosphorus atoms; 2 lack phosphorus atoms. Prior to the bug fix, only 12 nucleotide balls were shown.
September 22, 2014: Version 2.2 with signed Jmol/JSmol version 14.3.7_2014.09.20.
1. A new dialog, Isolate, will be found between the previously available Hide and Find (near the bottoms of the first three tabs). Isolate makes it easy to hide everything except one entity. Isolate can be used in combination with Hide, in either order.
2. Molecular animations are demonstrated in Powerpoint®. These animations for Powerpoint were generated with the PolyView-3D Server recommended in Presenting Views from FirstGlance, which can be accessed from a link at the bottom of the lower left panel in FirstGlance.
  
  Improved:
3. Hide can now hide atoms with halos (namely, atoms that were given halos with Find). This is useful when multiple copies of the same thing need to be hidden. For example, 1or9 is an 18-chain assembly. (Use Java for this large structure.) Each chain has a helical domain and a globular domain. To hide all 18 globular domains, Find sequence range "61-199". Then Hide atoms with halos.
4. Hide now informs you when you try to hide something that is not present in the model. (Previously, it said nothing while the molecular view remained unchanged.)
5. The term chain is now linked to an explanation.
6. An explanation of backbone traces was created in Proteopedia, and linked wherever backbone traces or ribbons are mentioned.
7. In the Chain Details help (Molecule Information Tab), individual chains can now be highlighted by clicking on the chain name.
8. The Vines view now remembers its checkboxes until the end of a session.
9. For biological unit models from the MakeMultimer server, the help was improved for Biological Unit under the Resources tab.
10. For NMR models, the help was improved for Local Uncertainty under the Views tab.
11. The "smaller ligands+" checkbox in the ligands+ button help is now remembered for the duration of a session.
12. A change in Jmol long ago has been causing the initial zoom to be too high when Jmol is rectangular. This has been fixed (set zoomLarge false).
13. Alternate locations are now discussed in the help for the Vines view, where they can best be seen.
14. The Gallery has some new cases (1ijw, 3hyd and 3if7).
15. The text in the Snapshot Gallery was updated. The snapshots themselves have not yet been updated.
  
  Bugs fixed:
16. Centering of the visible atoms often did not work. (Thanks to Bob Hanson for fixing this bug in Jmol.)
17. The tool Salt Bridges / Cation-Pi Interactions failed to warn that some interactions are not shown when relevant amino acids are missing, or have incomplete sidechains. The new warning has a yellow background.
18. The Crystal Contacts and Unit Cell tools now behave appropriately for models that lack crystallographic information, including homology models from Swiss-Model, biological units from MakeMultimer, and models from the Orientations of Proteins in Membranes server.
19. Homology models from Swiss-Model, when uploaded, generated a large spurious alert message.
20. Homology models from Swiss-Model, when uploaded, had a garbled report in the molecule information tab.
21. Some models from the Orientations of Proteins in Membranes server (available in the Resources Tab) had garbled reports in the molecule information tab, and also produced a large spurious alert during loading. Example: 4fz0.
22. Models from the Orientations of Proteins in Membranes server (available in the Resources Tab) contain pseudo-atoms marking the predicted boundaries of the hydrophobic portion of the lipid bilayer. In the View: Vines, with more detail checked, when the ligands were hidden with the Ligands+ button, pseudo-atoms close to protein remained visible as erroneously covalently bonded to protein.
23. Hide, Atom: when the atom was calcium (e.g. 4aqr) some results were incorrect.
24. Reset was resetting most things even when canceled.
25. Reset was not obeying the spin preference.
26. Reset was not turning the Quality button off.
27. The "smaller water" checkbox in the water button help was being remembered but not being obeyed.
June 12, 2014: Version 2.1 with signed Jmol/JSmol version 14.0.17_2014.06.11.
1. Preferences:
  - Spinning when the session begins is now optional.
  - When using JSmol, you can hide the suggestions for browsers that perform better. Exceptions:
    - Because the performance of Internet Explorer with JSmol is unacceptably slow, the suggestion not to use it cannot be hidden.
    - Because rotation in Opera is unacceptably slow/jerky, the suggestion not to use it cannot be hidden.
  - When using JSmol, you can hide the recommendation to use Java for better performance.
  Improved:
2. Help and explanations have been clarified in several places, especially for Crystal Contacts (Tools tab).
  
  Bugs fixed:
3. Atoms that were hidden were nevertheless reported when touched with the mouse (onMouseOver), or clicked. This caused mis-identification of atoms, and selection or hiding of incorrect moieties with mouse clicks. (Jmol bug, thanks to Bob Hanson for the fix.)
4. Water hydrogen atoms were inappropriately displayed when present in the model (1lcd, 1lfa). (Jmol bug, thanks to Bob Hanson for the fix.)
5. The Contacts & Non-Covalent Interactions Tool was not working when the PDB file lacked standard header information. Thus it was not working with uploaded PDB files such as homology models, biological units from MakeMultimer, etc. Thanks to Eugenia Polverini (University of Parma, Italy) for calling this bug to my attention.
6. In the Contacts & Non-Covalent Interactions Tool, selecting a sequence range starting with the higher sequence number and finishing with the lower sequence number did not work.
7. The number of missing residues reported was incorrect when there are multiple models (e.g. 2q3o). The sum for all models was reported rather than the number missing in the first model.
8. The "Get Biological Unit" buttons were going to a submission form instead of the final result for the current PDB code, due to a change at the MakeMultimer server.
9. PDB files lacking SOURCE records caused FirstGlance to fail to load.
10. Clicking on a water oxygen atom incorrectly identified it as "(main chain)". This has been fixed for both HOH and DOD (deuterium oxide).
11. The amino acids graphic chart was not displayed in the section on amino acids in the Notes.
April 27, 2014: Version 2.00 with signed Jmol/JSmol version 14.0.13.
Version 2.00 mostly concerns making the use of JSmol (no Java, the new default) more user friendly.
1. Default: no Java. This version defaults to using no Java (using JSmol and HTML5). Because JSmol (no Java) is significantly slower than Jmol (Java), a "BUSY" message appears over the molecule while commands are processed. Jmol (Java) remains an option in Preferences, or with a checkbox at FirstGlance.Jmol.Org.
2. Browser advice: The Chrome browser is recommended when using JSmol because it has the best performance. Internet Explorer (extremely slow overall) and Opera (very slow rotation) are discouraged. Recommendations appear in yellow banners, and can be seen, without installing multiple browsers, by spoofing a particular browser:
3. Preference: A new tab Preferences has a checkbox to set using Java (Jmol_S, the signed Jmol applet) as the default. Query parameters &JAVA or &NOJAVA override this preference. The checkbox at FirstGlance.Jmol.Org uses query parameters.
4. Large molecules: When the model contains 10,000 atoms or more, using Java (Jmol_S, the signed Jmol applet) is recommended for better performance.
5. Multiple models: When using JSmol (no Java), and when the data file contains multiple models (typically for NMR experiments), only the first model is loaded. This avoids overloading JSmol. Currently there is no "View All Models" capability when using JSmol, but this is planned for a future version of FirstGlance. When using the Jmol_S signed Java applet, all models are loaded, and "View All Models" is available.
6. Installing and Enabling Java has been explained in detail for Windows and OS X and all popular browsers.
  
  Bugs fixed:
7. The Labels Front checkbox was not working.
8. Some links to Troubleshooting were broken.
January 5, 2014: Version 1.98 with signed Jmol/JSmol version 14.0.4.
Version 1.98 is a major upgrade: the Jmol Java applet is now always signed. Optionally, FirstGlance will run without Java using JSmol.
1. Signed Java Applet. This version defaults to the signed Jmol applet. This was done because Oracle has announced that unsigned Java applets will soon be prohibited for security reasons.
2. Without Java. This version can also operate with JSmol, instead of the Jmol Java applet. JSmol does not require Java, which has become increasingly problematic. (The JS in JSmol stands for javascript.) Performance (smoothness of rotation, speed of responses) is somewhat diminished in JSmol, but adequate except for the largest structures (thousands of atoms).
  Bugs fixed:
3. "Center visible chains" was not always working.
4. Some hydrogen atoms, and one nitrogen in histidine, were not being colored in the Charge view. (Protein amino terminal charges are still not shown due to difficulty in identifying them.)
5. When a standard residue occurs as a ligand, the count reported in the Molecule Information Tab included occurrences in protein or nucleic acid, not just ligand (e.g GLY in 3f4j, 4cpa; A in 1bkx).
  OCA:
6. Uses of OCA removed in version 1.95 have been restored.
July 7, 2013: Version 1.951 with Jmol applet version 13.0.15.
1. The signed Jmol applet is used for Mac OS 10.6 (Snow Leopard), Mac OS 10.5 (Leopard), and Mac OS 10.4 (Tiger). This works around what appears to be a bug in Java version 1.6.0_51. This change does not affect Windows or Mac OS 10.7 or later, which use Jave 1.7.
June 16, 2013: Version 1.95 with Jmol applet version 13.0.15.
1. Two new Tools, Crystal Contacts and Unit Cell, have been added. Further options for these views are planned, but the basic views appear to be working.
2. A new View, Solid, has been added. It is the same as the initial view in the tool Contacts & Non-Covalent Interactions, but with a new explanation and examples.
3. The molecule information tab now has a line about the presence or absence of hydrogen atoms in the model. It is linked to a new help panel with details, and an introduction to hydrogen atoms in PDB files.
  Enhanced:
4. Hydrophobic/Polar (Views tab) was improved. Cys is now deemed hydrophobic. Most importantly, non-standard amino acids are colored white (formerly magenta).
5. Local Uncertainty (Views tab) now gives the minimum, average, and maximum temperature for each chain, water, ligands+, and hydrogen. The chain with the lowest average temperature among a group of sequence-identical chains is highlighted in boldface.
6. Slab now has a 20% thickness option, as well as the previously available 10%, 6%, and 3%. Also there is a new checkbox which unhides the back of the molecule, so you can see the inside of a cavity or channel.
7. The report by Disulfides/S/Se is more detailed and includes a count of sulfur in non-standard residues. There are also many more examples listed in the help.
8. Instructions for obtaining Biological Units now offer a backbone only model, useful when the all-atom model exceeds Java memory.
  Bugs fixed:
9. Some buttons (such as Spin and Background) were sometimes inappropriately canceling centering, hiding, or target selection in Contacts.
10. Non-standard amino acids were being colored "polar" (magenta) in the Hydrophobic/Polar view. They are now white.
11. Some selenocysteines were not being counted by Disulfides/S/Se.
12. Selenium and iron (Se, Fe), when clicked, were being inappropriately described as "Epsilon, 5th".
13. OCA has been out of service for weeks, so some links that use OCA have been removed or directed to other services. Removed: FASTA sequences, OCA under Resources. Redirected: View PDB file now fetches from RCSB.
May 5, 2013: Version 1.92 with Jmol applet version 13.0.13.
1. The Hide.. and Find.. tools are now available in all four tabs (at the bottom). Thanks to Frieda Reichsman for this suggestion.
2. Secondary Structure (Views tab) now reports the percentages of helix, strand, and neither.
3. Charge (Views tab) now reports the numbers of positively and negatively charged amino acids with incomplete sidechains, in addition to the total numbers. The counts now exclude hidden residues and alternate locations and include the carboxy termini. Previously carboxy termini were overlooked in the Charge view, but now they are colored red for negative charge. (Amino termini are more complicated and will be added in a later version.)
4. Atoms with alternate locations, when they occur, are now reported in the Molecule Information Tab, with a tool to find them. Examples: 3hyd, 1bsz.
  Changes:
5. The initial background is black instead of white, to make the "empty baskets" for missing residues more visible.
6. The Spin, Background, etc. buttons have been rearranged to make them more consistent between tabs.
  Bugs fixed:
7. Hide and Find were missing from the molecule tab when the molecule lacks a proper PDB file header (such as PDB files from MakeMultimer or Orientations of Proteins in Membranes).
April 23, 2013: Version 1.9 with Jmol applet version 13.0.13.
Version 1.9 is a major upgrade of FirstGlance in Jmol.
1. Controls have been reorganized into 4 sections, each with its own tab: Molecule, Views, Tools, and Resources.
2. The initial view now marks regions with missing residues with an "empty basket" (see image at right). The empty baskets can be hidden with a checkbox in the Missing Residues report, available from a link the Molecule Tab.
3. The molecule tab (titled with the PDB code when applicable) offers information from the "header" of the PDB file:
  1. Name of the molecule.
  2. Dates of deposition and release.
  3. Method of structure determination.
  4. Resolution, R value and free R. Resolution and free R are graded by FirstGlance to help novices interpret these values.
  5. Asymmetric unit:
    1. The number of chains, and the number of sequence-distinct chains. Clickable chain names identify the location of each chain.
    2. Details about each chain including its length, whether protein, DNA or RNA, presence of non-standard residues.
    3. Sequences are easily accessible from links to various sequence databases. (There is still no clickable sequence-to-structure listing -- it remains under development.)
    4. The total number of missing residues. Also a summary table listing the residues missing in each chain, and their sequence numbers, and the number of charged residues that are missing. (The S2C "gaps" server is no longer necessary.)
  6. The biological unit is readily accessible.
  7. Ligands and non-standard residues are listed with their counts and full names. Clicking on one shows its position(s) in the model.
  8. The publication abstract at PubMed is one click away.
  9. All literature citations given in the PDB file are listed, with clickable PubMed ID and DOI links.
  10. The PDB file text is one click away.
4. The Views Tab offers display and color schemes that affect the entire structure. It includes the 8 views previously available, plus Local Uncertainty (formerly under More Views) with expanded help and options.
5. The Tools Tab offers tools that identify, highlight, or measure specific substructures: Disulfides/S/Se, Salt Bridges/Cation-Pi, Contacts, Distances/Angles, and Advanced/Technical. None of these are completely new but there are some new options and expanded explanations.
6. The Resources Tab offers guidance for use of servers external to FirstGlance, some of which were formerly available under "Key Resources". Guidance has been greatly expanded. In addition to the previously featured resources (biological unit, evolutionary conservation, and Proteopedia), there is now guidance for all-atom clash analysis with MolProbity, prediction of intrinsically unstructured regions of protein chains, and marking of lipid bilayer boundaries for integral membrane proteins.
7. Hide.. and Find.. are now available at the bottoms of any of the four tabbed control panels. There are some new capabilities in these tools:
  1. The Find.. tool now finds amino acid or nucleotide sequence fragments, e.g. sequence=skek or sequence=cgg.
  2. The Hide.. tool now asks whether you wish to hide all copies of the residue/group or atom you clicked, or only the single one clicked.
8. Formerly, FirstGlance showed structures but did not report counts. This version, for the first time, reports counts, e.g. number of chains, amino acids and nucleotides, missing residues, ligand groups, non-standard residues, disulfide bonds, sulfur atoms, selenium atoms (selenomethoinine and selenocysteine), positive and negative charges, and numbers of atoms/residues found with the Find.. tool.
9. Bugs fixed:
  - In the Hide.. tool, with the range option, formerly when the higher sequence number was clicked first, hiding failed.
  - In the Hide.. tool, with the Atom option, the red list of atoms hidden inadvertantly included the XYZ coordinates of the atom (evidently due to a change in Jmol). Also clicking the same atom twice (possible even after it is "hidden" in some displays) was not properly handled.
  - In the Find.. tool, there were problems when the query included a single quote, as in *.c5'.
  - The Backbones checkbox in Contacts Shown was not being remembered.
February 13, 2013: Version 1.47 with Jmol applet version 12.2.34.
1. Operation in the Internet Explorer 9 web browser has been restored after failing for several months. (Operation in Internet Explorer 7 and 8, Firefox and Chrome never failed.) Operation in IE9 was accomplished with the following restructuring:
  - FirstGlance now uses Jmol.js for the first time.
  - The division layout (file fg.htm) was restructured following the resizable Jmol scheme kindly provided by Angel Herráez.
2. Java security risks and recommendations for using Java safely have been documented.
3. Zoom help was expanded to include moving the cursor to the right inside edge of Jmol. Mac: ; Windows: .
4. A link to Mouse Use was added beneath Jmol, along with a link to Java Security.
5. Updated list of compatible browsers and notes on browser peculiarities.
June 17, 2012: Version 1.46 with Jmol applet version 12.2.30.
1. The cutoff distance for van der Waals interactions in the Contacts display has been reduced from 4.5 Å to 4.0 Å at the recommendation of several crystallographers. See Van der Waals interactions.
2. Using Advanced Options (at firstglance.jmol.org, or by clicking New Session within an existing session) you can request the signed Jmol applet. This version of Jmol's signed applet enables writing a .jmol file that contains everything (including the state script and the atomic coordinates) needed to regenerate the view at the time the .jmol file was written. The .jmol file can be dragged into the Jmol application, or the signed applet. To write a .jmol file, click on Jmol at the lower right of the molecule to open Jmol's menu, then open the Console. In the lower white box, issue the command "write filename.jmol".
Minor Interim Upgrades (dates noted below):
1. Options for visualizing Biological Assemblies have been expanded to include the MakeMultimer Server, and to caution about the frequent apparent errors at the PISA server. (These changes were added to version 1.45 on May 7, 2010.)
2. Added a color key to Color by Uncertainty (under More Views..).
3. In Contacts.., added a caution that salt bridges and cation-pi interactions are shown only for protein.
4. A method for calculating pI and charge at various pH values was documented, and linked into the Charge.. dialog. (This and the previous two changes were added to version 1.45 in May/June, 2011.)
5. Added more information under "How Does It Work?" in What Is FirstGlance in Jmol?.
6. Noted in Adoptions that Nature discontinued direct 3D View links to FirstGlance as of the September 23, 2010 issue. (This and the previous item were added to version 1.45 in February, 2012.)
April 14, 2010: Version 1.45 with Jmol applet version 11.8.22.
1. Under More Views.. is a new dialog to show disulfide bonds clearly, as well as to show cysteine residues not participating in disulfide bonds. Also cys residues can be labeled.
2. Under Key Resources.. PQS (Probable Quaternary Structure) has been updated to use PISA, as well as offering PQS and RCSB for obtaining biological assemblies.
3. Some progress was made in preparation for translation to other languages, but FirstGlance is still not translation-ready.
February 4, 2010: Version 1.44 with Jmol applet version 11.8.17.
1. Jmol now resizes automatically with the browser window.
2. Added Key External Resources, replacing the 4 buttons "PQS, PDB, OCA, Gaps?". New on the list are Proteopedia, Evolutionary Conservation, and MolProbity.
3. Changed Secondary Structure. It now represents beta strands and sheets in a more realistic fashion -- gone are the straight planks shown in earlier versions. Also the ribbons are a bit narrower in Cartoon.
4. The initial view for Charge.. is now to color only the charged atoms. All the previous options remain available.
5. Status HPUB at the PDB, or an invalid PDB code, is detected, and explanatory help should appear automatically. (A similar feature was present in version 1.02, but was later broken by changes at the PDB, and regardless, had not been installed in versions higher than 1.1.)
6. Incorporated links to Proteopedia.Org in several places, with explanations of why it is useful in a particular context.
7. Limitation removed: Atoms can now be identified with Slab on, due to improvements in Jmol. Identification is by clicking on the atom (which reports at the lower left of Jmol) or by touching the atom, which reports in a yellow "hover" box. Slab mode can also be used in the Contacts and Hide dialogs now.
8. Protein atom identifications now include "main chain" or, for sidechain atoms, the greek letter, spelled out in English.
9. Included "Atom" in hover report (e.g. "...Element=C, Atom=C7"). It was previously included in the identification report produced by clicking on an atom.
10. The extensive Notes document was updated throughout. Some more technical documents have not yet been updated, but are marked as out of date (e.g. those listed under Technical Information for Programmers).
11. Bug fixed: thymidines were erroneously labeled as having incomplete sidechains "S-" due to a change in nomenclature with the remediated PDB format (t.c5m is now t.c7).
12. Bug fixed: A351 in 1bkx is not covalently bonded to any other nucleotide. It was not displayed within the "ligands+" group as intended.
13. Bug fixed (I think): FirstGlance occasionally failed to complete loading. This was found to happen when the server supplying the visitor count (sitemeter.com) failed to respond. The meter code was put inside a division, which appeared to permit loading even without a response.
14. Bug in Jmol fixed: in "Center Atom" mode, clicking on Jmol's background no longer causes a zoom out.
15. Bug in Jmol fixed: hydrogens on charged sidechain nitrogens are now colored blue in the Charge.. display, "color only charged atoms". Formerly they were white.
16. Adoptions was updated to include Protein Science.
17. Work was begun to prepare FirstGlance in Jmol for translation to español and other languages.
April-December, 2008: Version 1.40-1.42 with Jmol applet version 11.5.20.
Limited release for the Epitopia server.
1. Added graphics Quality toggle button.
2. Added support for the Epitopia Server.
3. The Adoptions page was updated to include Proteopedia and TOPSAN.
4. Updated help for taking snapshots for presentations.
September 15, 2007: Versions 1.39 (for OCA and ConSurf/Pepitope/Selecton with Jmol applet 11.3.11)
and version 1.01 (at firstglance.jmol.org, Jmol applet remains 10.2.0).
1. Fixed a bug that prevented hiding (in Hide..) or selecting (in Contacts..) chains of DNA. This bug was created when the Protein Data Bank changed the PDB format on August 1, 2007, in accord with their data remediation project. Specifically, the former nucleotide names A,C,G,I,T,U now designate only RNA, while DNA nucleotides are named DA,DC,DG,DI,DT,DU.
2. Fixed a bug that prevented the Labels: Front checkbox from working. This had resulted from a change in Jmol. (This fix applied only to version 1.39.)
Limited Releases*, April-August 2007: Versions 1.36-1.38.
1. Support for the Pepitope Server.
2. Support for the Selecton Server.
3. *Version 1.36 [April 7, Jmol 11.1.27] and 1.37 [April 13, Jmol 11.1.27] were installed at only the Pepitope and Selecton servers. Version 1.0 (Jmol 10.2.0) remained installed at firstglance.jmol.org, and version 1.2 (mislabeled 0.995, Jmol 10.2.0) remained at ConSurf and OCA.
4. * Version 1.38 [August 27, Jmol 11.3.11] was installed for Pepitope, Selecton, and at the OCA server (used for uploading PDB files saved from Pepitope or Selecton jobs). Version 1.0 (Jmol 10.2.0) remained installed at firstglance.jmol.org.
5. In Jmol 10.2.0, calcium was incorrectly classified as protein. This bug was fixed in later Jmols, enabling the removal of the workaround in FirstGlance that was needed previously.
6. Preliminary support for submitting a Jmol state script to generate high-resolution images at the ConSurf Server only.
7. Added Polyview-3D to Presenting Molecular Views. (August 6, 2007)
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. Version 1.0 remains the main public version at this time.
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.
4. Since version 0.991 is now version 1.0, version 0.995 should have been called version 1.2.
5. Version 0.995 (1.2) is public, at this time, only at the ConSurf Server and OCA. (The version at OCA was updated to 0.995 to support upload of saved ConSurf job PDB files.)
August 23 - September 3, 2006: Version 0.995 (with Jmol applet version 10.2.0).
1. This version was released at the ConSurf Server and OCA Servers only. It was not released at firstglance.jmol.org pending further improvements. Release at the OCA Server was to support display of saved and uploaded ConSurf PDB files.
2. Added support to display evolutionary conservation results from the ConSurf Server.
  - This involved the first use of messageCallback from Jmol to javascript, which enabled the following change, and will enable future enhancements.
3. The "Please Be Patient!" help that appears at the beginning of a session is now automatically replaced with the Introduction after the molecule appears.
4. Moved the visitor count from the "Please Be Patient!" help (which now may disappear so quickly the count might fail to load) to beneath the molecular view (scroll down).
5. Added a new link to the control panel: New Session.
6. The Charge.. default color scheme has been changed to make it easier to see the distribution of charged atoms. The old 5-color scheme remains available via a checkbox.
7. One of the new Charge.. views shows only charged atoms. Because some crystallographic models have incomplete sidechains, where the charged atoms are missing, these are detected and indicated.
8. Hide.. has a new option to hide a range of residues within one chain (or multiple such instances). This is similar to the range-targeting function previously available in Contacts.
9. Hide.. has a new Invert Hiding checkbox. Previously hidden moieties are displayed, and vice versa. This makes it easier, for example, to view a single chain out of many (first hide it, then invert hiding).
10. Added instructions for copying static snapshots of molecular views and pasting them into presentations or documents. The new instructions are linked to the bottom of every help panel.
11. Bug fixed: In Hide.., the option to Center Visible Chain was not working reliably.
12. Bug fixed: Following a Reset, certain operations (such as Center Visible Chains in Hide..) had inappropriate consequences (such as an inappropriate start of spinning, or failure to center properly).
13. Bug fixed: After showing Contacts, and then using Center Atom.., clicking Return to Contacts failed to clear centering mode.
14. Bug fixed: Jmol defaults to showing hydrogen bonds for rare PDB files. These are now hidden with an explicit "hbonds off". An example is 4MDH (in FGiJ 0.991). See Jmol Bugs.
15. Clicking the "Zoom Up" button no longer intereferes with target selection for Contacts, and does not interfere with hiding a range of residues, by displaying its help.
16. Added a color key for the element-colored displays of salt bridges and cation-pi interactions (under More Views..).
17. Added the journal Molecular Biosciences to the Adoptions page.
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 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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