2.32 (October, 2015) through the current version remain operational in Java and
1.98 (January, 2014) through 2.31 remain operational in JSmol/HTML5 mode only.
The Java mode cannot be used without updating Jmol
due to the unintentional revocation of Jmol's certificate for Jmol versions before October 15,
0.95 (November, 2005) - 1.951 remain on the server. These use the unsigned Java applet.
They will display molecule files ending ".pdb" in the Gallery, but
but do not fetch PDB codes because the method in use back then has been removed from the
bioinformatics.org server. Some of the earliest versions don't work even for
".pdb" items in the gallery because they use the
signed applet and the certificate was revoked.
A list of version numbers is below. To use a previous version, add the version number after
"/fgij" in the URL. For example,
July 7, 2016:
Version 2.51 with JSmol/signed Jmol version 14.6.0_2015.05.24 (second version marked
with this date, actually released May 27, 2016).
When saving animations while using Java, sometimes the saving fails with
"ERROR: capture canceled". A way to prevent this has been documented, and help
now appears automatically when this condition arises. See
When using JSmol, PDB files are fetched from the Protein Data Bank (rcsb.org)
via a small program, jsmol.php. This program has now been implemented on the
bioinformatics.org server. Previously FirstGlance was using jsmol.php at stolaf.edu.
The change means that a rare out-of-service occurrence at stolaf.edu will not
prevent FirstGlance from working.
Item #22 under Bugs Fixed for version 2.5 was not fixed correctly. Also, the bond
not shown in the example given there was between the main chain N of Thr198 and the carboxy
carbon of Asn197, not the bond with NAG697.
May 31, 2016:
Version 2.5 with JSmol/signed Jmol version 14.6.0_2015.05.24 (second version marked
with this date, actually released May 27, 2016).
Version 2.5 enables saving images and presentation-ready animations.
Static images and animations can now be
saved directly from FirstGlance in Jmol. Animations can be
360 degree rotations, or rocking, and will display as animations in presentations (e.g. Powerpoint,
free Google Slides or Libre Office) or in web pages.
Examples of animations saved from FirstGlance are provided:
FirstGlance can now be used to save a presentation-ready animation of any
molecular scene in Proteopedia.
Instructions are provided.
Proteopedia's easy-to-use Scene Authoring Tools (see the
can be used to customize rendering and coloring, and the customized scene
can then be saved as a presentation-ready animation.
The total number of atoms in the model is now reported in the Molecule Information Tab.
The chemical elements in the model are now reported in Molecule Information Tab, with
a link that shows the counts of each element, and enables finding an element in the model.
When the model includes selenium (Se), you are referred to Disulfides/S/Se in the Tools tab.
When the model includes selenomethionine (MSE), a link is provided to an explanation. Example:
Enolase, an enzyme in glycolysis, colored by evolutionary conservation,
has been added to the
Gallery under ConSurf Examples.
The help for Asymmetric Unit/Biological Unit now tells you if you are looking
at the asymmetric unit. Thanks to Stacy Tchouangouem for this suggestion.
In Contacts & Non-Covalent Interactions (Tools tab), in the help panel (lower left),
the element color key has been moved up to a more visible position.
Instructions for testing old versions of FirstGlance are now included
at the top of this document.
Center Atom, when using Java, froze Jmol_S starting in FirstGlance 2.4.
Thanks to Bob Hanson for help locating this bug.
Crystal Contacts and Unit Cell (in the Tools tab) were not working
when using Java, starting in FirstGlance 2.4.
Clicking an atom when displaying
Crystal Contacts or Unit Cell (in the Tools tab)
reported the Element in multiple copies.
Clicking on Be (beryllium) in 4znl, or Se (selenium) in 4hik reported "(Epsilon, 5th)".
Certain large models were showing red crosses on every water in the initial view
Clicking on atoms with lower case chain identifiers failed to generate a report
In Contacts & Non-Covalent Interactions (Tools tab), some covalent bonds between
the target and contacting atoms were not being shown consistently. Example: in 1g9m, the covalent
bond between NAG697 and ASN197 was not being shown unless Show hydrophobic interactions
January 14, 2016:
Version 2.42 with JSmol/signed Jmol version 14.4.1 update 2015.12.23.
In the Find.. dialog, the report of atoms found failed to be displayed
in Version 2.4.
January 7, 2016:
Version 2.41 with JSmol/signed Jmol version 14.4.1 update 2015.12.23.
Version 2.4 broke the help panel (lower left panel) for Center Atom, Thin Backbone, N->C Rainbow
(and perhaps others), showing "undefined".
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.
Clicking on an atom now reports the chemical element in addition to the atom ID.
The element was previously reported in the hover message.
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.
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.
Triple clicking seems to be needed for distance/angle measurements (only when using Java).
The Tools tab Distances/Angles help now mentions this.
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.
* Recommendations are more urgent when the molecule has >10,000 atoms, e.g.
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:
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.
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.
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).
The Reset button in the ConSurf control panel did not restore the gray
color of backbones of chains not colored by evolutionary conservation.
The 4 views were displaying unwanted water due to remediation in the Protein Data Bank
which assigned chain names to water.
ConSurf was reporting sequence identity between some non-identical chains (e.g. chains A
and P in 2vaa).
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).
The ConSurf Colors checkbox was inappropriately greyed out for some Views
(e.g. Thin Backbone).
The ConSurf Colors checkbox was inappropriately greyed out when
Sequence Numbers or Residue Names checkboxes were used.
The Isolate tool in the FirstGlance control panel was turning off ConSurf coloring.
Dots in view 3 remained yellow after view 2.
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.
Dots were not being shown around the balls and sticks of ligands.
Other Bugs fixed:
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!
Center visible moieties in the Hide.. dialog was broken in FirstGlance
October 19, 2015:
Version 2.32 with signed Jmol/JSmol version 14.4.0 update October 17, 2015.
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:
The certificate for the Jmol Java applet was inadvertantly revoked on October 15, 2015,
causing operation of all earlier versions to be denied.
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.
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.
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
June 16, 2015:
Version 2.3 with signed Jmol/JSmol version 14.3.7_2014.09.20.
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.
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.
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.
Putting halos on some atoms (with Find..) caused the automatic centering to fail
when using Isolate...
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.
Reset was not resetting the Labels checkboxes (bottom of every tab except Preferences).
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.
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
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.
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
In the Chain Details help (Molecule Information Tab), individual chains
can now be highlighted by clicking on the chain name.
The Vines view now remembers its checkboxes until the end of a session.
For biological unit models from the MakeMultimer server, the
help was improved for Biological Unit under the Resources tab.
For NMR models, the
help was improved for Local Uncertainty under the Views tab.
The "smaller ligands+" checkbox in the ligands+ button help is now
remembered for the duration of a session.
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).
Alternate locations are now discussed in the help for the Vines view, where they can best be seen.
The Gallery has some new cases (1ijw, 3hyd and 3if7).
The text in the Snapshot Gallery was updated. The snapshots themselves have not yet been updated.
Centering of the visible atoms often did not work. (Thanks to Bob Hanson for
fixing this bug in Jmol.)
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.
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
Homology models from Swiss-Model, when uploaded, generated a large
spurious alert message.
Homology models from Swiss-Model, when uploaded, had a garbled
report in the molecule information tab.
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.
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.
Hide, Atom: when the atom was calcium (e.g. 4aqr) some results
Reset was resetting most things even when canceled.
Reset was not obeying the spin preference.
Reset was not turning the Quality button off.
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.
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.
Help and explanations have been clarified in several places,
especially for Crystal Contacts (Tools tab).
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.)
Water hydrogen atoms were inappropriately displayed when present in
the model (1lcd, 1lfa).
(Jmol bug, thanks to Bob Hanson for the fix.)
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.
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.
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.
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.
PDB files lacking SOURCE records caused FirstGlance to fail to load.
Clicking on a water oxygen atom incorrectly identified it as
"(main chain)". This has been fixed for both HOH and DOD (deuterium
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.
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
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:
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.
Large molecules: When the model contains 10,000 atoms or more,
using Java (Jmol_S, the signed Jmol applet) is recommended for
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"
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.
Signed Java Applet.
This version defaults to the signed Jmol applet. This was
done because Oracle has announced that unsigned
applets will soon
be prohibited for security reasons.
This version can also operate with
instead of the Jmol Java applet.
JSmol does not require Java, which has become increasingly
Performance (smoothness of rotation, speed of responses)
is somewhat diminished in JSmol, but adequate except for the largest
structures (thousands of atoms).
"Center visible chains" was not always working.
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.)
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).
Uses of OCA removed in version 1.95 have been restored.
July 7, 2013:
Version 1.951 with Jmol applet version 13.0.15.
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.
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.
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.
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.
Hydrophobic/Polar (Views tab) was improved. Cys is now
deemed hydrophobic. Most importantly, non-standard amino acids are colored
white (formerly magenta).
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.
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
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.
Instructions for obtaining Biological Units now offer a backbone
only model, useful when the all-atom model exceeds Java memory.
Some buttons (such as Spin and Background) were sometimes inappropriately
canceling centering, hiding, or target selection in Contacts.
Non-standard amino acids were being colored "polar" (magenta) in the
Hydrophobic/Polar view. They are now white.
Some selenocysteines were not being counted by Disulfides/S/Se.
Selenium and iron (Se, Fe), when clicked, were being inappropriately
described as "Epsilon, 5th".
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.
The Hide.. and Find.. tools are now available in all
four tabs (at the bottom). Thanks to Frieda Reichsman for this suggestion.
Secondary Structure (Views tab) now reports the percentages
of helix, strand, and neither.
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.)
Atoms with alternate locations, when they occur, are
now reported in the Molecule Information Tab, with a tool
to find them. Examples: 3hyd, 1bsz.
The initial background is black instead of white, to make the "empty
baskets" for missing residues more visible.
The Spin, Background, etc. buttons have been rearranged to make them
more consistent between tabs.
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.
Controls have been reorganized into 4 sections, each with its own tab:
Molecule, Views, Tools, and Resources.
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.
The molecule tab (titled with the PDB code when applicable) offers
information from the "header" of the PDB file:
Name of the molecule.
Dates of deposition and release.
Method of structure determination.
Resolution, R value and free R. Resolution and free R are
by FirstGlance to help novices interpret these values.
The number of chains, and the number of sequence-distinct chains.
Clickable chain names identify the location of each chain.
Details about each chain including its length, whether protein,
DNA or RNA, presence of non-standard residues.
Sequences are easily accessible from links to various sequence databases.
(There is still no clickable sequence-to-structure listing -- it remains
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.)
The biological unit is readily accessible.
Ligands and non-standard residues are listed with their
counts and full names. Clicking on one shows its position(s) in the model.
The publication abstract at PubMed is one click away.
All literature citations given in the PDB file are listed, with
clickable PubMed ID and DOI links.
The PDB file text is one click away.
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
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.
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
Hide.. and Find.. are now available at the bottoms of any
of the four tabbed control panels. There are some new capabilities in these
The Find.. tool now finds amino acid or nucleotide sequence fragments,
e.g. sequence=skek or sequence=cgg.
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.
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.
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
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
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:
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
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
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.)
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,
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.
Notes document was updated
throughout. Some more technical documents have not yet been updated,
but are marked as out of date (e.g. those
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.
September 15, 2007:
Versions 1.39 (for OCA and ConSurf/Pepitope/Selecton with Jmol applet
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.)
*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
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.
Jan 14: Added
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.
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
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
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
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
May 10, 2006: Version 0.991 (with Jmol applet version 10.2.0).
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.
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
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
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.
More Views.. has a new option to show all salt bridges
and cation-pi 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"
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
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
which links to the "SEQRES to Coordinates" alignment (S2C) resource by
Wang and Dunbrack.
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 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).
PDB files can now be uploaded for display in FirstGlance in Jmol.
There is a new option on the main page to do this.
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.
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
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
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
Display more detail: all non-water atoms as sticks,
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
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
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.)
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
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
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
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 a free
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 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.
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.