- February 13, 2013:
Version 1.47 with Jmol applet version 12.2.34.
- 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:
-
Java security risks and recommendations for using Java safely
have been documented.
-
Zoom help was expanded to include moving the cursor to the right inside
edge of Jmol. Mac:
; Windows:
.
- A link to Mouse Use was added beneath Jmol, along with a link
to Java Security.
- Updated list of
compatible browsers
and notes on
browser peculiarities.
- June 17, 2012:
Version 1.46 with Jmol applet version 12.2.30.
- 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.
- 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):
-
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.)
- Added a color key to Color by Uncertainty (under
More Views..).
- In Contacts.., added a caution that salt bridges and
cation-pi interactions are shown only for protein.
- 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.)
- Added more information under "How Does It Work?" in
What Is FirstGlance in Jmol?.
- 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.
- 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.
- Under Key Resources.. PQS (Probable Quaternary Structure) has
been updated to use PISA, as well as offering PQS and RCSB for obtaining
biological assemblies.
- 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.
- Jmol now resizes automatically with the browser window.
- Added Key External Resources, replacing the 4 buttons "PQS, PDB,
OCA, Gaps?". New on the list are Proteopedia, Evolutionary Conservation,
and MolProbity.
- 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.
- The initial view for Charge.. is now to color only the charged
atoms. All the previous options remain available.
- 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.)
- Incorporated links to
Proteopedia.Org in several places, with explanations
of why it is useful in a particular context.
- 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.
- Protein atom identifications now include "main chain" or, for sidechain
atoms, the greek
letter, spelled out in English.
- 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.
- 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).
- 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).
- Bug fixed: A351 in 1bkx is not covalently bonded to any other
nucleotide. It was not displayed within the "ligands+" group as intended.
- 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.
- Bug in Jmol fixed: in "Center Atom" mode, clicking on Jmol's
background no longer causes a zoom out.
- 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.
-
Adoptions was updated to include Protein Science.
- 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.
- Added graphics Quality toggle button.
- Added support for the
Epitopia Server.
- The Adoptions page was updated to include Proteopedia
and TOPSAN.
- 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).
- 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.
- 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.
- Support for the
Pepitope Server.
- Support for the
Selecton Server.
- *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.
- * 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.
- 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.
- Preliminary support for submitting a Jmol state script to generate
high-resolution images at the ConSurf Server only.
- 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).
- 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.
- Jan. 14: Added
What Is FirstGlance in Jmol? (Thanks to Phil Leader
for suggesting this.)
- 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.
- Since version 0.991 is now version 1.0, version 0.995 should have
been called version 1.2.
- 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).
- 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.
- Added support to display evolutionary conservation results
from the ConSurf Server.
- Support for ConSurf increased the size of FirstGlance by
about 25% (from 15K lines in .htm and .js files to 20K). Most of the
code was adapted from Protein Explorer.
More..
- This involved the first use of messageCallback from Jmol to javascript,
which enabled the following change, and will enable future enhancements.
- The "Please Be Patient!" help that appears at the beginning of a session
is now automatically replaced with the Introduction after the
molecule appears.
- 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).
- Added a new link to the control panel: New Session.
- 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.
- 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.
- 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.
- 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).
- 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.
- Bug fixed: In Hide.., the option to Center Visible Chain
was not working reliably.
- 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).
- Bug fixed: After showing Contacts, and then using
Center Atom.., clicking Return to Contacts failed to
clear centering mode.
- 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.
- 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.
- Added a color key for the element-colored displays of salt bridges
and cation-pi interactions (under More Views..).
- Added the journal Molecular Biosciences to the
Adoptions page.
- May 10, 2006: Version 0.991 (with Jmol applet version 10.2.0).
- 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.
- New Exit buttons were provided for Hide.. and Center
Atom.., replacing the former exit links.
- At the main page, enabled pressing Enter (in addition to clicking the
Submit button) to submit a PDB code to start a FirstGlance session.
- 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.
- 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.
- Fixed several bugs that prevented the PDB identification code
from showing, to the upper left of the molecule, after the background
color changed.
- Minor improvements/corrections in documentation.
- May 3, 2006: Version 0.99 (with Jmol applet version 10.2.0).
- 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.
- 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.
- A new Snapshot Gallery was
provided.
- More Views.. has a new option to show all salt bridges
and cation-pi orbital interactions throughout the molecule.
- 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..).
- 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.
- Hide Hydrogen was added to the Hide.. interface.
This enables uncluttering ligands or non-standard
residues. (Example:
1AL4 has hydrogen on both.)
- 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.
- 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.
- 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.
- Most links and buttons now display pop-up help when the
mouse is held over them for a few seconds.
- 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.
- Slab thickness can now be controlled (3 steps).
- The definition of "carbohydrate" was greatly improved (for
the "hide carbohydrate" checkbox). See
- Rare Anomalous atoms
are no longer invisible, but are shown as
dots.
- Hidden atoms are now listed by element, sequence number, and chain,
rather than by serial number. (Serial number is used internally.)
-
Specifications for a future interactive sequence listing were developed.
- 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.
- The help for N->C Rainbow now includes a spectral color sequence.
- Added a "mascot" image to the main page.
- 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.
- 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).
- 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.
- 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.
- Added a PQS "button" in the control panel (upper left panel,
near the PDB and OCA buttons).
- More Views.. now includes a new section on evaluating
model quality, with "color by temperature"
(thanks to Gale Rhodes)
and a link to MolProbity.
- More Views.. now includes checkboxes to show the
axes, unit cell, or bound box.
- More Views.. now includes a link for visualizing
dipole moments in Jmol.
- Added 1IGT (antibody) to the Gallery to provide an example with
disulfides in multiple chains, and both inter- and intra-chain disulfides.
- Fixed a bug in Vines.., Hide Sidechains that failed to hide
the sidechains in nucleic acids.
- Korea was added to the list of mirror
sites.
- The advanced option to use browser frames was discontinued.
- February 2-12, 2006: Version 0.97 (with Jmol applet version 10.00.48).
- 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.
-
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).
-
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.
- Disulfide bonds are shown by default in the initial view,
in all backbone trace views, and in Vines.
- New entries in the Gallery illustrate disulfide bonds and
non-standard residues.
- 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.
- In the Vines.. display,
there are now (in the help panel) new checkboxes
to
- Hide sidechains.
- Display more detail: all non-water atoms as sticks,
- Hide hydrogen.
- In the Ligands+ display,
there is now (in the help panel) a new checkbox
to display smaller ligands+ atoms.
- When water is displayed,
there is now (in the help panel) a new checkbox
to display smaller water atoms.
- 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.
- 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.
- Turning centering off after
a single centering click was not possible, because in "set picking center"
mode, Jmol 10.00.46 does not call pickCallback(). Using "center atomno=" instead
of "set picking" could have avoided this, but it caused unwanted changes
in zoom.
- 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.
- 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.)
- Known unresolved issues was revised,
and unimplemented plans for future enhancements were added.
-
Several
mirror sites are now listed.
- 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).
- The link to Protein Explorer, formerly in the upper left
control panel, has been moved to the More Views.. help section.
- 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.
- Adjacent to the PDB link, a graphic link to the
OCA
Browser Atlas entry has been added.
-
Fixed bug that reversed the Charge cationic/anionic colors in
the color key. (These colors were never reversed in the molecular view.)
- Fixed bug that reversed the Solvent and Ligand colors
in the Composition view. (Thanks to Frieda Reichsman for pointing
out this bug.)
-
Tested dozens of potentially problematic PDB files, documenting the
results. See links at the bottom of
About FirstGlance.
- 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).
- 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.
-
Added additional information at the bottom of
Technical Information for Developers.
- 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.
Feedback to