Protein Explorer: Versions

Protein Explorer
© 2000 by Eric Martz

Design Features
Known Limitations
Version History
Future Plans

This section lists design features which may not be obvious when using the Protein Explorer.

Cookies are Used. The Protein Explorer (PE) uses cookies for convenience. Cookies are not a security hazard and can be disallowed if desired.
Automatic NMR Model Counting. When multiple-model NMR files are loaded, they are detected automatically by querying Chime for the model count. The Explore! screen will offer an additional option "Select NMR Model" which brings up a special control panel for NMR model selection. This is made possible because my requests to have Chime automatically detect NMR PDB files and behave accordingly, and to add the NMR model count to Chime's 'show info' report, were kindly implemented in Chime 2.0 by Tim Maffett of MDL Information Systems, Inc..
PDB Files via Internet Gzipped. When PDB files are obtained directly from a PDB mirror site via Internet (without first saving the PDB file to the local disk), PE uses a URL at the PDB which transmits the PDB file in gzipped form. This typically reduces transfer time by nearly four-fold. Originally, this was made possible because Jaime Prilusky kindly implemented my request to offer this option from the Brookhaven PDB in 1998. Subsequently, Helge Weissig kindly implemented a similar capability at the RCSB PDB. The trick to taking advantage of Prilusky's enhancement is to use "send-x-pdb" (e.g. www.pdb.bnl.gov/pdb-bin/send-x-pdb?id=9dna) instead of the more usually used "send-pdb" (e.g. www.pdb.bnl.gov/pdb-bin/send-pdb?id=9dna). Also, the former sends the file with MIME type chemical/x-pdb (which can invoke RasMol or Chime) whereas the latter sends the file with MIME type text/html, so it is displayed as text in the browser.
For the RCSB, the URL to fetch a gzipped PDB file for 9dna is: www.rcsb.org/pdb/cgi/export.cgi/9dna.pdb?pdbId=9dna&format=PDB&compression=chime
Javascript Can Query Chime Unambiguously. A mechanism is implemented which, for the first time (12/98), allows javascript unambiguously to query Chime (see shared\cquery.js). It is used, for example, to ascertain whether or not an NMR PDB has been loaded, and if so, to ascertain the model count (see above). The mechanism sends a script to Chime and then parses the result from Chime's message stream. In order to be sure the correct messages are parsed, the script is enclosed between unique marker comments.
Busy Status. PE's javascript now knows when Chime is busy (has not completed a script). The mechanism is that an 'end of script' comment is added as the last line of every script before it is sent to Chime (see top.EOS in shared\s2c2.js and explorer\top_vars.js). Since the messages are now guaranteed to come back in correct order (after unscrambling, see below), javascript knows that Chime is finished when the end-of-script comment comes back. The busy status is used to avoid sending additional scripts to Chime before the execution current script has been completed. In the case of sending 'interrupt' followed by an additional script, failure to wait until each script has completed can result in the intermingling of commands from different scripts in the message stream, a condition the present unscramble() routine is not able to deal with.
Javascript also knows when Netscape is busy, namely, when a document in a frame has not completed loading (busy status is turned on by onUnload and turned off by onLoad). This avoids clicking on links or buttons before all the relevant forms and documents are in place.
The Explorer (one molecule at a time) has a Ready/Busy indicator below Chime. The Comparator does not have such indicators but internally obeys the same rules. This is because the Comparator would need three separate indicators (one for each Chime and one for Netscape) and this seemed not worth the effort for programming nor the screen space required nor the visual distraction from three indicators.
Chime's Messages are Unscrambled. The above capability requires a mechanism to unscramble the order of messages received from Chime (see version 0.95). This was made possible because, at my request, Tim Maffett kindly implemented a mechanism to enable unscrambling. Maffett determined that the scrambling I had reported to MDLI occurs in the plug-in/Netscape interface, and is therefore not under the control of MDLI (and is not a bug in Chime). The mechanism he provided is to add a sequence number to each message sent from Chime to javascript. I was then able to write a javascript unscramble() function (which required over 400 lines of code exclusive of comments!).
To see the unscrambling in action, issue the command "javascript top.db(true)", which turns on a debugging mode. All messages will now be reported to the message window, prefixed by S (for Scrambled) and then U (for Unscrambled).
Temporary disconnect for loops. The unscrambling function requires that out-of-order messages be stored until they can be passed out in order. The NMR [Auto] (automatic display of each model in sequence) uses a looped script which can easily generate thousands of messages. Unlike some non-looped scripts, there is no need in this case for javascript to "scrutinize" the text of each message. Therefore, a special mode was provided in unscramble() for looped scripts -- in this mode, message numbers only are unscrambled, without storing the messages themselves or passing them onto the message text processing function. When every message number is accounted for, and the interrupt has been processed, Chime has completed the script. However even this took too long (javascript being an interpreted language) and after a long period of viewing the [Auto] loop, and after Chime had processed the interrupt which stops the loop, it would take many minutes for unscramble() to process even just the message numbers. During these minutes the user must wait while nothing appears to be happening. (Actually unscramble() is going at top speed but nothing happens on the screen and the user is locked out by the "busy" condition.) Therefore a third mode was implemented, called disconnect mode, to make the [Auto] loop display recover quickly after an interrupt. In disconnect mode, message numbers as well as message texts are simply discarded. After sending the interrupt, a reconnect operation is initiated. In order to determine when Chime is idle/ready, this function checks at one-second intervals and turns off the "busy" flag only after a second in which no messages were sent by Chime. This may not be a bullet-proof method but is the best I've come up with. The worst consequence could be that left-over messages might come back unexpectedly after reconnect signals that Chime is "ready". This would likely generate an illegal condition in unscramble() which would then recommend closing the window (ending the session).
Stopping on a known model number. During automatic stepping through a series of NMR models, a desired function is to interrupt on any model and have the javascript report which model you chose. A Chime script command "javascript top.show_model(N)" is used to update the model number shown as each new model is displayed in Chime (see auto_model() in nmr.js). The problem is that when the delay between model stepping is short (< 0.25 sec on my Pentium 150 MHz) these commands execute in scrambled order, showing incorrect model numbers. The above strategy of disconnecting the unscrambling process during automatic model stepping complicates this problem. My solution is that even when unscrambling is disconnected, unscramble() watches for comments of the form #@NN, where NN is the current model number. By keeping track of the model number associated with the highest message number seen, the model number at interrupt is known. This is written into the form slot to ensure that the display is correct after the interrupt (see after_reconnect() in nmr.js, and reconnect in shared\unscramble.js), and more importantly the image is regenerated for this model number to guarantee that the model number shown in the form slot is the model number displayed in Chime. This seems to work satisfactorily.
State Maintenance. It is possible to change the documents in any frame without losing the state of the system. This is accomplished by having all state variables (top_vars.js and top_cmpv.js) in the top-level frameset, rather than in any particular document. These variables survive throughout the entire session. It is also convenient to have the shared javascript functions in the top-level frameset. This avoids having references to these functions break when structural changes are made during enhancements.

The following limitations remain in version I plan to fix these as time permits.
Chime 2.6 provides "show pdbheader", but Protein Explorer does not yet utilize the newly available PDB file header, e.g. to provide buttons to highlight residues listed in SITE records.
Scripts saved from Chime lack surfaces and other rendering features introduced since RasMol. A script recorder is under development that will solve these problems.
MSA3D: Long multiple protein sequence alignments may result in excessively slow listings (over 30 min) and cannot be stopped once started. Alignments over 32K bytes in length won't fit in the form box. A solution has been designed and is being completed.
The Sequence and Seq3D displays show nonstandard residues as gaps. I shall attempt to implement an alternative method of querying Chime for sequence information, which avoids this problem.
Failure of chain color scheme for NMR ensembles. When there are multiple models, the "chain color scheme" built into Chime assigns each model a different color. Since (in non-expert mode) FirstView shows only the first model, multiple chains will all be the same color (blue).
Fixing the following limitations is not worth the time required, so these are expected to remain indefinitely.
Buttons may get confused. When certain states are changed with manually issued commands, or from Chime's menu, related buttons may lose track of the status of the image. For example, if you change the display of the hetero atoms, or toggle spin with the menu, the [Hetero] and [Spin] buttons won't know this. The only consequence is that you may have to push these buttons two or more times to get the desired result.
One Auto-Model at a Time in the Comparator. The [Auto] button on the NMR Model Selection screen toggles automatically through all NMR models, showing one at a time. At present, in the Comparator, there is no mechanism to allow running [Auto] concurrently in both Chimes. This would require additonal javascript code to distinguish the busy status of each Chime and behave accordingly. Currently, there is only one busy status flag (top.chime_busy) which can be set by either of the Comparator's two Chimes or by Netscape with onUnload.

Future Plans
The following new features are planned or in preparation for future releases of PE, but are not yet available for beta testing. We are optimistic that these will become available in future releases since we have received NSF funding through 2004. If one of these features would be especially useful to you, or if you may be interested in collaborating on development of one of these features, or if you have an idea for a feature not listed below, please contact me.

Prespecification of initial view and description. A mechanism to allow a hyperlink to prespecify not only the molecule(s) to be loaded, but also the initial view(s) to be shown, and the initial descriptions. This will allow an illustration in a textbook to become the first image within PE (same rendering and color scheme), with chapter and page reference and customized initial description. The mechanism will be to include the url to a javascript file (on a web server) as a query parameter in the link to PE. The js file will contain all customized information in a standard format.
Presentations within PE. A template for building presentations within PE. The presentation format will be similar to that for which a template has been offered for several years. By being within PE, the command line and all other PE capabilities will be available to manipulate any image in the presentation.
Full utilization of information in the PDB Header. At present, I have found no simple mechanism to access the PDB Header text in javascript. A mechanism will be developed to allow this (java applet or CGI). PE can then offer highlighting in the 3D structure based on information in header records such as SITE, CISPEP, SEQRES, HETNAM, SSBOND, LINK, HYDBND, SLTBRG, and perhaps others.
Hydrogen bonds. A mechanism to locate and display all hydrogen bonds, including buttons to show categories such as backbone-backbone, backbone-sidechain, sidechain-sidechain, interchain, water bridges. Preliminary work has been done in collaboration with Mike Sauder, using the HBPLUS package of Janet Thornton with her permission.
Open platform for third party enhancements. A mechanism to allow anyone to create a control page (upper right frame) within PE. This would allow information available from a third party database or calculation to be intergrated into PE, providing buttons to highlight the contributed information.
Model Quality. Links and help for novices to assess model quality.

Version History

April 24, 2001: Version 1.86 Beta.

A new glossary, index, and help document has been begun. It is accessed by clicking the green circled question mark at the title of any control page , or from the Molecule Information Window. It will take a few more releases until this is reasonably complete.
Information available in the Molecule Information Window has been enhanced, and now includes

An introduction to the EBI Probable Quaternary Structures site, with examples and a link to the PQS page for the current molecule.
An introduction to crystal contacts, with examples, snapshots, a Chime presentation on the case of malate dehydrogenase (where crystal contacts appear to affect conformation), and a method for generating a PDB file for visualizing crystal contacts using DeepView and RasMol.
Methods for obtaining fewer or single chains from PQS, ExPASy's ExPDB, or with RasMol.
A link to the KUN/WHATIF PDB Report for the current molecule, giving information on the model quality.

Thanks to Steve Johnston (Whitehead Inst.) for pointing out that the molecule information icon didn't look like a button. It does now.
QuickViews Plus (at the bottom of the QuickViews menu page) has a new checkbox to include all models in the contact surface rendering. This supports the display of crystal contacts, using PDB files having the asymmetric unit in model 1, and the crystal contacts in model 2.
The DISPLAY menu of QuickViews has a new option: Vine.
The Contact Surfaces controls (in the middle help frame) in QuickViews have a new option, to display the surface as dots. This is especially useful for small ligands and drugs.
The Contact Surfaces display of QuickViews has been enhanced to show single non-bonded atoms as small spheres. For example, a water molecule near the surface may produce proximity coloring, but be non-bonded (not a large ball) if there are no possible hydrogen bonding donors or acceptors beneath the surface at that position. Formerly, such a water molecule was not rendered at all.
Some typographical errors in the salt bridge report (linked to the help frame in QuickViews) were corrected.

March 16, 2001: Version 1.85 Beta.

Animation of ensembles of models has been greatly enhanced. Access is via Advanced Explorer, under NMR Models/Animation. The button formerly labeled [Auto] is now labeled [Animation].

Faster than before, without crashing (previous versions crashed often). Speed limited only by size of the PDB file.
Several displays and color schemes can now be selected for animations.
The animation can be saved as an html file and played back later in Netscape, without running Protein Explorer. A title can be specified.
Animations can be zoomed, centered, have stereo toggled, or have background toggled while running.
Delays at the ends of animations are now optional (Ends checkbox).
Custom animation scripts may now be divided into an initialization block (run only once, specifying the color scheme and center) and a loop block (displaying each frame). This improves speed and allows initialization of orientation, centering and zooming, yet permits orientation, center or zoom to be changed while the animation is running.
Animation scripts are displayable, for copying and use in constructing presentations.
A single PE session can open multiple animations concurrently.
Different PE sessions can open animations concurrently.

An introduction to animation, with several examples of morphs (some new) and ensembles simulating thermal motion, is accessed by clicking on the animated GIF on the FrontDoor, or from the help buttons (blue question marks, circled) on the NMR Models/Animation page.
A slot was provided on the FrontDoor page for pasting a URL to a PDB file on a server. Pressing [Go] then starts PE to load this PDB file from the server. Examples are provided to try out.

March 11, 2001: Version 1.81 Beta.

A new QuickTour guide has been added. At this point, only the first of several sections has been completed. This is designed to enable a beginner to learn how to visualize the fundamental structural features of a protein in about an hour.
The order of items on the QuickViews DISPLAY menu has been revised. "Center" was removed since it is superceded with the [Center] button.
An additional option for the QuickViews Contacts display (in the help panel) displays atoms "inside + outside" the surface. This shows covalent bonds (if any) between the two groups.
QuickViews: After SELECT, Nucleic, the "distinguish DNA from RNA" routine has been enhanced to show the counts of pentose C2' and ribose O2' (in the message box). These counts make it easy to check whether every C2' has or lacks an O2'. Also, it now leaves "nucleic" selected upon completion.
The QuickViews help for the [Ligand] button now mentions how to look up the full name for a 3-letter ligand abbreviation in the PDB header.
The QuickViews help for HBonds now includes a figure with information about typical lengths of hydrogen bonds.
A new guide to troubleshooting Chime and PE has been provided.

December 29, 2000: Version 1.80 Beta.

A new option has been added to the QuickViews menus: SELECT Clicked. Atoms, residues, or chains can be selected with mouse clicks.
In the QuickViews Contacts display, the Contacts help frame includes new links to many options: make the surface transparent, hide it, restore it; hide the non-contact portions of the surface; show or hide the atoms bonded to, or 7 Å from, either side of the surface. There are also convenience links to change the color of water, and show thin backbone traces. All these links select the corresponding atoms, for use in subsequent DISPLAY or COLOR menu operations.
In the QuickViews Plus Options, changing the diameters of DISPLAY modes now automatically updates the image.
Fixed (we think) the dreadful bug that reported Fatal error -- this is not your fault. This problem occurred only during startup of PE (not during a session after successful startup) and only on rare computers (mostly fast Win2000 or WinNT systems), but on those it sometimes happened in most startups. None of the computers used for development (including one fast Win2000 system purchased with the intent of debugging this) showed the bug often enough to debug it. Thanks to Tim Driscoll for trapping information that enabled this to be fixed.

November 14, 2000: Version 1.72 Beta.

Spin control. People were observed letting one or more spinning sessions go into the background, resulting in their computer performance being severely degraded -- "freezing". A new warning cascade has been implemented to urge people to stop spinning when they don't need it. Nevertheless, if you want a demonstration to spin permanently, this is easily achieved by canceling both warnings.
Shared folder verification. During startup, PE now verifies that the shared folder exists, and that the files therein are of the same version as PE itself. If not, it explains what to do.
Colored with DRuMS icon button links were added where appropriate.
The small black window offering more information about MSA3D in Netwatch, Science Sept. 1 2000, no longer pops up every time the FrontDoor is loaded.

October 4, 2000: Version 1.71 Beta.

Fixed a bug that prevented PDB ID codes from being loaded (Ouch!). The bug incorrectly reported that Chime 2.0.3 was not installed when in fact it had been. Also fixed another bug that caused the PDB ID code slots on the FrontDoor page to fail to work (Ouch!). These bugs were first introduced in version 1.7.
Offered, to teachers, answers to the tutorial study questions (see link at top of study question page; study questions are accessed from the tutorial, which is accessed from the link on the FrontDoor page, under About PE).
For Macintoshes, improved sizing of the message window vs. frame size.

October 1, 2000: Version 1.7 Beta.

Revision of the Tutorial has been completed, and more Tutorial Study Questions were added.
Quickviews Plus Options have been added to the bottom of the QuickViews page. These change the logic between consecutive SELECT and DISPLAY operations, and allow control of the thicknesses of backbones, traces, sticks, and the radii of spacefilled spheres.
More predefined protein terms are included in the SELECT menu (which has been reorganized), and the help for such selections offers Kurt Gile's Venn diagrams of these terms.
More plain colors were added to the QuickViews COLOR menu.
Access via proteinexplorer.org was established.
The zoom alias z has been changed to Z because the lower case alias interferes with the command rotate z {angle}.
Many miscellaneous minor bugs were fixed, and minor improvements made.

September 7, 2000: Version 1.485 Beta.

The first half of the Tutorial has been revised to reflect the major changes in this version. Work to complete the revision continues at high priority (since I'm teaching a class from it that began, coincidentally, Sept. 7, 2000). The tutorial is currently linked to the main entry page (index.htm), and to the About PE page accessible from the copyright notice on all pages. More explicit links to the tutorial will be reinstated in a future version.
Tutoral Study Questions have been provided in a separate document.
The Advanced Level Form for Recording Observations has been expanded.
The document listing why PE is easier to use and more powerful than RasMol was revised.
A Center button has been added to the convenience button bar accessible from all pages. Thanks to Tim Driscoll for this suggestion. (To conserve space, the Seq3D link was deleted from the button bar. Seq3D can be accessed from the Molecule Information Window.)
New QuickViews DISPLAY options are HBonds and SSBonds.
New QuickViews SELECT options are Helices, Sheets, Hydrogen, Inverse, and Clicks. The latter allows form-based control of measurement of distances, angles, dihedral angles, display of monitor lines (with or without distances), and labeling atoms with custom labels and fontsize.
A new adjunct to the QuickViews SELECT menu is a menu of boolean operators (And, Or, Not) to relate the forthcoming selection to the previous one. This will probably be moved to the bottom of the QuickViews page in a future version to unclutter the top, as additional options are likely to be added (e.g. adding a display mode to the existing display of the selected atoms, rather than replacing the old display mode with the new).
The "Unable to allocate shade" and resulting miscoloring now produce an alert, directing the user to COLOR >Help<, where a fix is explained.
A (Repeat) option has been added to the QuickViews SELECT, DISPLAY, and COLOR menus. It re-executes the previous selection. Thanks to Tim Driscoll for this suggestion.
Seq3D can now accumulate selections, allowing any arbitrary set of residues or ranges to be selected easily.
Netscape 4.08 is the earliest version now compatible with PE. Earlier versions of PE allowed 4.04. Netscape Communicator 4.75 is recommended. (Communicator 6 remains incompatible with Chime!)
Miscellaneous minor bugs were fixed, and minor improvements to documentation were made.

August 10, 2000: Version 1.481 Beta.

The project folder is now set with a browse button. This avoids mistyping the path and other problems. (See the link "Project Folder" below the message box.)
Miscellaneous minor bugs were fixed.

August 1, 2000: Version 1.48 Beta.

Cation-Pi interactions and Salt Bridges can now be displayed automatically, either from QuickViews' DISPLAY menu, or from Advanced Explorer's new Cation-Pi/Salt Bridge branch. A tutorial is provided, which includes a gallery of snapshots.
MSA3D has been improved, tested much more thoroughly and further debugged. It now has an option to display the sequence alignment in black and white (for printing). Sliding adjustments can now be specified at multiple points. A tutorial has been provided.
QuickViews SELECT menu has a new option: Element.
When changing between the top and bottom molecule in Comparator, the QuickViews frame no longer has to reload in order to update the list of chains on the SELECT menu. Thanks to Tim Driscoll for telling me how to do this!
Numerous other bug fixes and small improvements were made.

June 16, 2000: Version 1.47 Beta. Special thanks to Paul Stothard whose permission to use his alignment scripting and coloring code greatly accelerated development of the MSA3D enhancement.

MSA3D. Molecules can now be colored according to conservation/mutation frequency based on an externally prepared multiple protein sequence alignment. MSA3D is a feature of Advanced Explorer.
Seq3D. The rendering controls in the top frame of Seq3D have been simplified.

June 3, 2000: Version 1.46 Beta. Special thanks to Frieda Reichsman and Tim Driscoll who suggested many of the improvements in this version.

New Entry Pathway. The lead-in pages have been further streamlined. One page has replaced three. Starting at index.htm, it takes only two clicks to enter Protein Explorer.
Session Name. Each PE session (window) is given a name automatically, which includes the PDB ID code if prespecified. The session name can be edited before entering PE, and appears at the top edge of the Netscape window. If several sessions are open concurrently, the session name assists in selecting the desired window to bring to the foreground.
Troubleshooting for PDB file network transfer. When PDB files are requested through the Internet, if they don't arrive within 30 sec, a troubleshooting window opens automatically. This explains how to change the PDB mirror URL being used, and how to cancel the session cleanly without waiting for the molecule to arrive.
The FirstView page was put into more logical order.
The Record of observations form was split into two forms, basic and advanced level, and provided also as PDF for easier printing.
Nucleotide Sequence Colors Fixed. Previously, in the sequence or Seq3D listings, nucleotides were colored as though they were amino acids. Now the DRuMS color scheme for nucleotides is used by default, and checkboxes are available to disable coloring for selected nucleotides.
Redundant chain names bug fixed. Frieda Reichsman brought to my attention some PDB files which have several chains with the same chain name. An example is 1acb which has three chains named "E", cleaved from a proenzyme chain. PE's Sequence and Seq3D interfaces now work properly with such files.
Comparator Windows reset bug fixed. In Windows Comparator, a reset initiated with the bottom molecule selected loaded the top molecule into both positions. This is fixed.
A new color scheme, polarity2 was added (in addition to polarity3 and polarity5).
Self-closing of accessory windows. Most accessory windows which can be opened in PE now close themselves automatically when the top level session window is closed. The Molecule Information window still does not automatically close (bug to be fixed in future).
Invisible molecule bug fixed. A bug was fixed that made the FirstView invisible for a certain variant of PDB file format for micromolecules (coming from the Woodcock site at Okanagan U).
Miscellanous. A number of small enhancements were made, including enhanced scope of the expert mode selectable under Preferences.

May 22, 2000: Version 1.45 Beta.

New Entry Pathway. The lead-in two pages have been redesigned. The second page now contains examples of several ways in which PE may be entered, most prespecifying the molecule(s) to be loaded. More importantly, the sequence of information and controls during entry have been redesigned. It is now anticipated that in most cases the molecule(s) will be prespecified by a hyperlink to PE. If no molecule is prespecified, PE immediately offers the Load Molecule page.
FirstView Description. The first page seen after loading a new molecule now contains extensive documentation about the intial view, including explanations of backbone rendering; water, hetero atoms and CPK colors, and disulfide bonds. This leads into the next page, the "QuickViews" control page.
QuickViews. An entirely new interface for manipulating the view has been provided called "QuickViews". It is designed to make it as easy as possible for novices to use simple select/render/color/center operations to manipulate the view, without knowing any Chime/RasMol command language or the terminology for predefined atom sets. It includes extensive explanations and help which appear automatically in a new (4th) frame. Over 5,000 words of help have been added for the QuickViews interface.
Molecule Information Button. A new molecule-information button icon appears on all pages as part of the convenience button cluster. It pops up a window which displays the brief description of the molecule (from the PDB HEADER and COMPND records), shows its PDB ID code, and provides links to display the PDB file header, the RCSB Structure Explorer page for this entry, and the amino acid/nucleotide sequence.
Sequence. A new display of the loaded molecule's one-letter amino acid or nucleotide sequence has been provided. Individual amino acids or groups with similar properties can be optionally color highlighted in the sequence listing. Touching a residue with the mouse displays its chain, 3-letter code, full name, and one-letter code mnemonic. Examples are listed illustrating a range of sequence irregularities, including gaps and insertions, and how to interpret them. The Sequence display is a wide display which covers the molecule, since it does not interact with 3D structure. In contrast, a more abbreviated display, Seq3D, leaves the molecule visible for interaction.
Seq3D. A new interactive sequence-to-3D interface has been provided. The sequence of the loaded molecule is displayed in one-letter code. Clicking on a residue or range of residues changes the rendering and color scheme according to user-selectable options. A [Seq3D] button is included in the button group on every page.
Startup vs. New Window. Startup has been redesigned. All startup is now via the single entry point pe.htm, which automatically opens a new window only when needed. If the hyperlink to pe.htm designates a target window which does not exist (thereby opening a new window for PE), PE detects and uses this window (history.length == 1, top.history.length == 1, top.frames.length == 0). If not, PE detects that it is in an old window or frame, and automatically opens a new window for itself. PE's Quit button always closes the top window containing PE.
Concurrent Sessions. When the link to pe.htm does not open a target window, pe.htm automatically opens a new window for PE. In this case, each window is given a new name. This allows multiple PE windows to be open concurrently. Each PE session is titled with the PDB id code or filename if prespecified, making it easy to find the desired session when several are running concurrently. See Construction of Hyperlinks to Protein Explorer. Now the Noncovalent Bond Finder can be operated concurrently with Protein Explorer.
The option to Resize the window before PE starts has been redesigned. It now works on Macintoshes as well as Windows. New query parameters allow links to bypass the default option to resize the window, and (if a single molecule is prespecified) to bypass the default option to specify a second molecule, thereby invoking the Comparator. The documents about starting PE from hyperlinks have been reorganized and revised, and are summarized in Constructing Hyperlinks to PE.
Button bar enhancements in the group of convenience buttons on every page. A new Reset button reloads the molecule, restoring PE's initial view. a Slab toggle button has been added. The Seq3D button (see above) is available on every page. The Synch button's action now toggles bidirectional following (available on Windows only due to bugs in Macintosh Chime and Netscape).
Changes in Button names/functions. The "Hetero" toggle button has been renamed to Ligand. The intermediate "dots" rendering of the Water button has been removed. The Water button now toggles simply between spacefill and invisible. Also the Water and Ligand buttons have been changed so that they preserves the previously selected atoms, rather than leaving water or ligand selected. The Bkg button now toggles simply between black and white (the intermediate gray background mode has been removed).
The Load Molecule page has been redesigned to offer its options more clearly, in a more logical order.
Expert mode. A new preference setting has been added for experts. When checked, some help intended for novices is not displayed. After a molecule is loaded, the "FirstView Description" page is automatically changed to the "Explore!" page, skipping the "QuickViews" page (which remains accessible from the "Explore!" page). In nonexpert mode, after 10 commands have been entered manually, the user is notified about the existence of expert mode.
Bidirectional NMR movies. A new checkbox was added to the NMR Model Selection control panel. It enables the series of models to play as a bidirectional movie. Previously, the movie could be played only forward.
Better error handling. I have tried to handle these conditions gracefully; that is, with an explanation and without a hang or a crash.

Invalid PDB ID codes. (Must be 4 characters beginning with a digit in the range 1-9). Examples: aaaa, aaaa + 1aa, 1d66 + d166.
PDB files with no sequence (no residues designated as amino acids or nucleotides). Example: 1tn1 or any micromolecule such as ATP.
"Chains" containing a single residue. (Their alpha carbons or phosphorus atoms are displayed as a ball to prevent them from being invisible in the initial backbone rendering.) Example: His tag, chain B in 1b07.

New command aliases have been added in each new version, but were not listed below. You can always see the complete list by clicking on the "Aliases" link under the message box.
Netscape Communicator 6 has been disallowed because it is currently incompatible with Chime 2.0.3.
Over a hundred other minor improvements and bug fixes were accomplished.

September 20, 1999: Version 1.0.

It took a year of work to achieve this version 1.0, yet it is far from finished. I have many plans for the Protein Explorer and will continue to develop it as fast as I am able. At present, it comprises over 10,000 lines of HTML, over 5,000 lines of javascript, and over 500 lines of RasMol/Chime script.
At long last, a first draft of the tutorial is finished. I did not feel it appropriate to assign the version number 1.0 to PE until it had a tutorial. The tutorial now contains links which run "movies" in the PE. A nice one is the first one under Hydrogen Bonds (27.A.ix). (You have to open the tutorial from within the Explorer in order for the movie link to work -- just click on the green question mark and go to Tutorial section 27.A.ix.)
A new control panel, Color Schemes, has been added, containing the two schemes which I considered most needed. Other schemes will be added in future releases.
A slot showing the count of atoms selected has been added below the molecular graphic in the Explorer (but not in the Comparator).
Disulfide bonds are now shown in the initial view immediately following loading, and the number of bridges is messaged. (With NMR files, an incorrect number of bridges is reported because inter-sulfur distances are scanned without regard to models -- a bug in RasMol/Chime.) SS bonds are also shown in the default view on the NMR Model Selection panel (one model at a time, correctly).
One-residue 'chains' are no longer invisible in the initial view. Alpha carbons and phosphorus atoms in nucleotides are now spacefilled in the initial view at a radius identical to the backbone radius. Thus they are invisible within the backbone of multi-residue chains. This was done so that one-residue chains are not invisible in the initial view -- they are now shown as tiny spheres (one must look carefully to see them!). There are over 90 PDB files containing one-residue 'chains' which are invisible if all 'chains' are rendered only as backbone. An example is 2csm.
Long load URL's. Chime 2.0.3 fixed a bug which prevented use of URL's longer than 70 characters in load commands in Windows. PE now allows long load URL's unless a version of Chime prior to 2.0.3 is installed. This problem affected mostly Windows (the limit on Macs is large enough not to cause many problems).
RCSB PDB. The above bug fix newly allows Chime to load PDB files from the RCSB servers. These have now been added to the "Record Preferred PDB Mirror" dialog.
A page demonstrating hyperlinks which pre-specify molecules from diverse third-party servers has been provided.
Resizing the window containing PE, or dragging the frame boundaries, is now better handled (with an onResize in shared/cmd2way2.js).
Further improvements have been made in fitting the command slot and message box optimally into various window sizes, and in the size of the molecular graphics frame relative to the control frames. Whether or not the command slot buttons appear next to it, or out of the way at the bottom, is a new preference.
As a convenience, focus is automatically returned to the command slot upon completion of many operations (any ready condition, all mouse clicks to identify atoms, the completion of any script).
http URL's allowed in script and load commands. "script" and "load" commands which use an "http://"-containing URL are now allowed even when a local disk project folder is not set. Note that load or script commands within the primary script must also use absolute URL's even for files in the same folder on the server. As a simple example of such a script, load and spacefill any protein, then paste this into your command slot and press enter:
script "http://www.umass.edu/microbio/chime/shared/cs_amphi.spt"

PE @ EBI. This version is compatible with the EBI Protein Quaternary Structure server, where (thanks to Kim Henrick) it is now offered as a viewer. For example, 2hhd.pdb contains only half of the hemoglobin tetramer; to view the entire tetramer in PE, go to pqs.ebi.ac.uk/pqs-bin/macmol.pl?filename=2hhd.
Help buttons have a new look.
PDB's via ftp. PDB files specified as query URL's from ftp servers are now handled correctly (provided the ftp server sends out the PDB file as chemical/x-pdb).
The default script for viewing single models on the NMR Model Selection page is now displayed in the help (press the [?] button after NMR Model Script, above the box). As explained in the help, this means you can paste it into the box and modify it.
A bug and a deficiency were fixed in the contact surfaces routines. A bug was fixed that prevented hydrogens from being excluded in ligand when requested. It was noted that unusual atoms, such as metals, were not being spacefilled in the receptor when within bonding distances. Hence, the "C/S" (carbon/sulfur) option was broadened to "C/S/X" (which click on to see more information).

August 3, 1999: beta-test version 0.992.

This version has been made capable of operating from the Protein Data Bank servers. The Protein Explorer decides it is on a PDB server when it finds itself being served from a directory path including the string "pdb/pe/". Therefore, this string should not be used in the installation path on non-PDB servers or local disks. When PE is on a PDB server, PDB files are fetched directly from the PDB cgi/export.cgi mechanism (http:///cgi/export.cgi/?comp=chime). Although the PE is being tested at the PDB, it will not likely be available on the public PDB beta server until September, nor on the production server until October or later (see acknowledgements).
In previous versions, molecules were always selected and loaded after entering the Explorer. This version offers automatic loading of pre-specified molecules upon entry. The molecules are specified with query parameters in the url, for example to fetch PDB ID 1d66 via Internet from a PDB mirror site,
www.umass.edu/microbio/chime/explorer/pe.htm?id=1d66
or to load a file from a local disk folder,
www.umass.edu/microbio/chime/explorer/pe.htm?id=c|/pdb/enzymes/1cbx.pdb&
The Comparator can be invoked by specifying two PDB ID's, for example
www.umass.edu/microbio/chime/explorer/pe.htm?id=1lck&id2=1b07
Detailed documentation is provided.
With the closing of the Brookhaven PDB site, the default source of PDB files via Internet has been changed to the former BNL PDB mirror at the Cambridge Crystallographic Data Centre, Cambridge UK. The three other former BNL PDB mirrors which currently provide the URL needed by PE to load molecules are also listed on the "change closest mirror" page (click the ? button next to the PDB ID slot on the "Load Molecule" page). Further information about the PDB, including PDB Lite access, is available at www.umass.edu/microbio/rasmol/pdblite.htm
The controls for generating surfaces and contact surfaces have been greatly expanded. Several internal checks have been implemented to avoid less informative results. A tutorial and documentation have been provided for the contact surfaces page. A preview snapshot of an exemplary contact surface is provided.
A new command to PE has been implemented, "tb". Prefixing a command with the word "tb" (short for "top + bottom") causes the command to be applied to both windows in the Comparator. An alias "sy" (short for "synch") was added which expands to "tb send mouse on", causing both windows to send mouse movements to each other (bidirectional mouse synchronization).
Earlier versions required Netscape 4.04 or later with javascript enabled and Chime 2 in order to enter the Explorer/Comparator. More thorough compatibility checking is now done, and more detailed instructions for achieving compatibility are provided. In this version, platforms other than Win32 and MacPPC are rejected (but an alternative solution is suggested), and java and cookies must be enabled before the client browser is allowed to start the Protein Explorer.

June 21, 1999: beta-test version 0.991.

PE 0.99 unnecessarily denied the use of long URL's to Macintoshes. PE now permits Macintoshes to use long URL's in "load" commands (>70 characters). Windows Chime 2.0.2 crashes Navigator with long URL's, so PE disallows such URL's for Windows.
Further improvements were made in sizing the command line slot and message box to fit various screen sizes.

June 16, 1999: beta-test version 0.99.

A list of features which make the PE easier to use and more powerful than RasMol has been added.
New control panels have been (partially) implemented for generating surfaces and contact surfaces colored by distance.
The tutorial has been partially drafted, and that part is included for what use it may be, incomplete though it is.
The bug which often prevented loading a molecule on the Macintosh has been fixed, I think. If any of these symptoms occur when you load a molecule on a Mac, let me know: the molecule fails to appear; error messages are generated in the message box; a permanent busy condition ensues. Also the [Clear] button now works to clear the message box on Macs.
A new preference controls whether molecules loaded are added to the 'Select previously loaded molecule' pick list.
The "show info" message is displayed upon loading a molecule.
A [Stereo] button has been added. You can set whether it toggles convergent or divergent stereo on the preferences screen.
The previous command can be recalled by typing "," (just the single character "comma"). "Comma" is the same as pushing the "Recall ^" button; "period" as pushing the "v" button.
A series of special "Commands to Protein Explorer" (as distinct from "Commands to Chime") have been implemented. All begin with a period followed by a single letter. These go directly to a desired control panel without a series of mouse clicks through intermediate panels. Press the [?] button next to the command line slot for the list.
The "NMR Model Script" is now remembered while you leave the "NMR Model Selection" control panel (including separately for the top and bottom molecules), but only within the session.
The command line slot, message box, and arrangement of the lower right frame now adjust in various ways to the size of the window to optimize visibility and usability. Best to resize the window BEFORE starting Explorer; else you need to Shift-Reload the lower right frame.

March 18, 1999: beta-test version 0.98.

Macintosh project folder. A bug was fixed which prevented the project folder mechanism from working on the Macintosh.
A menu delay was added so Chime's menu won't pop up unwanted on the Macintosh. Mac users should click on the "MDL" logo to get Chime's menu.

March 16, 1999: beta-test version 0.97.

Macintosh fixes. The following fixes were attempted for Macintoshes.

The [Synch] button in the Comparator is no longer present when used with a Macintosh because a bug in Chime 2.0 prevents it from working on Macintoshes (it works on Windows).
The frame(s) containing Chime should no longer have scrollbars.
After entering a command, the cursor should now return to the command slot. (If not, press Tab.)
When using Netscape 4.5 on a Mac, the preference "Add new messages at the bottom" defaults to checked. (If you have already used the Protein Explorer and entered the Preferences checklist, the settings present when you exited the Preferences checklist will not be changed.)

Netscape Toolbar eliminated. The window which opens for the Explorer/Comparator no longer has a toolbar, to discourage use of the [Back] and [Forward] buttons which don't work well in this context.
Atom Picking Reports Explained. A new preference has been added which, by default, attempts to explain/interpret the terse RasMol-style identifications reported when clicking on an atom.

February 4, 1999: beta-test version 0.96.

Purpose of the Protein Explorer. A new document entitled Purpose of the Protein Explorer has been provided with the rationale and some historical background.
Preferences. Several user-configurable preferences have been added. For example, you can specify that the initial view of newly loaded molecules not be spinning. Click on "Preferences" below the message box.
Command aliases. Command alias expansion has been implemented. For example, s l expands to select ligand. The list of aliases and replacements is user editable. Click on "Show aliases" below the message box for details.
Configurable project folder(s). It is possible to specify a "project folder" on your local hard disk. This means that all manually issued "load" and "script" commands will look for the referenced pdb and script files in the project folder. Click on "Set Project Folder" below the message box for details.
Add new messages at top or bottom. In Macintosh Navigator 4.5, the message textarea form element retains focus at the bottom of the message list, whereas in Windows and all previous versions for both platforms, focus remains at the top of the window. The default is to add new messages at the top of the window, so they are always visible for Windows. For Macintosh users of Navigator 4.5, this leaves the messages always out of view. Therefore a preference option has been provided which adds new messages at the bottom.
Force Ready. The Force Ready link under the message box now does what it says in one click. For example, resizing the window typically causes a permanent busy condition. Clicking once on Force Ready now cures this condition.
Shortening Chime-saved scripts. A new document was provided which describes how to shorten Chime-saved scripts. It is accessed from the "Set Project Folder" link below the message box.
Non-existent pdb/spt files. Attempting to load a non-existent PDB file or script from the local disk caused a permanent busy condition. The user is now alerted to click on "Force Ready" when necessary.
Structure message bug fixed. Using the menu to, for example, Color, Structure may cause the structure summary message list to be generated. These messages were not being handled properly, causing a fatal error. A similar condition occurred when "unable to allocate shade" color warning messages were emitted (for example after Color, Shapely). These messages now appear in the message box, and no fatal error is generated.

January 03, 1999: beta-test version 0.95.

Functions separated. The single upper right frame, which contained all controls, was getting too crowded and complicated. Therefore, PDB-file loading, NMR model selection, and Exploration have been separated onto different upper-right panels.
A new Message Control panel has been provided, accessed from the command-line/message-box panel in the lower right.
This version takes advantage of these enhancements in Chime version 2 (full release):

Multiple-model NMR files are now automatically detected and loaded accordingly. ("nmrpdb=1" is no longer needed in the embed tag for Chime.)
The following bug was fixed in Chime 2: in NMR mode, Chime 2-beta-4 was unable to run scripts from disk files.

Because this version depends on Chime 2's auto-detection of multiple-model NMR files, and the above bug fix, and since Chime 2 is now available for both Windows and Macintosh, Chime 1 is no longer supported.
Unscrambling of message order. The order of Chime's messages becomes scrambled when they are passed back to javascript for scripts of more than a dozen or so lines. This is true for Chime 1 and 2, and on both Windows and Macintosh. It is not a bug in Chime, but a peculiar interaction between Chime and Navigator which is not under the control of MDLI. The scrambling prevents javascript from obtaining script results unambiguously (for example atom counts following select commands, or the model count after loading an NMR file). A "workaround hook" was provided in Chime 2, namely, messages are now numbered. (See the RasMol email list history for '08 Nov 1998' for details.) Using these numbers, message order has now been unscrambled with a complicated javascript function (see unscramb.txt, unscramb.js and scrambld.txt; see also the description above under Design Features: Unscrambling).
Busy detection. A mechanism has been incorporated to prevent a script from being sent to Chime when it is busy processing the previous script, and to suggest that the user re-issue the request after waiting a few moments. The detection of busy-status for Chime requires the unscrambling mechanism mentioned above, and the addition to each script of a trailing "end of script" comment for detection in the returning message stream. See unscramb.txt.
Auto-detection of NMR model count. The unscrambling of message order (see item above) allows automatic determination of the number of models loaded when an NMR multiple-model file is loaded (see call to top.request_nmr_model_count() and render_view1() in loadit2.js). The entire process, which is tricky due to asynchrony between javascript and Chime, is described in a comment at the head of file cquery.js (Chime QUERY),which contains much of the relevant code.
New features on NMR Model Selection panel. Four new features were added. (i) The [Model] buttons can now step either forward ([Model+]) or backward ([-]). (ii) A new [Auto] button automatically steps through all models (or the models in the model list). Pressing the [Auto] button stops the progression, and reports the number of the model displayed when stopped. This allows one to determine the number of a selected model during the automatic stepping. (iii) A new Always show model black slot is provided. One model can remain displayed, in black, as a reference configuration, while stepping through other models with the [Model+][-] or [Auto] buttons. (iv) A new Model list slot is provided. Here one can list a series of model numbers, in any order. The [Model+][-], [Auto], and [All] buttons obey this series. Thus, one can step through any subset of the models in any desired order, or show any subset overlaid.
Mouse synchronization in the Comparator. A new [Synch] button, present only in the Comparator, forces the second molecule to follow mouse-directed movements of the first molecule. Thanks to Tim Maffett of MDLI who implemented this suggestion of mine in Chime 2.0.
Zoom convenience buttons. Although zooming can be done with the mouse (holding down the Shift key), the response is hypersensitive. Convenience buttons [Zoom^][v] were added which step the zoom either way in increments of 16% relative to the current size.
The default rendering of water is now spacefilled, rather than dot surfaces. The dot surfaces, and hiding water, are still available as steps on the cycle of the [Water] button.

October 18, 1998: beta-test version 0.92.

A slot has been provided which allows the user to specify script commands for any desired representation and color scheme for displaying NMR models. In the Protein Comparator, separate scripts can be specified for each molecule (top vs. bottom).
A number of minor bugs were fixed, and minor conveniences added, including a [Del] button to delete unwanted entries from the "Previously loaded PDB file" pick list.
Some non-obvious design features were documented, and information is provided about PE's use of cookies.

October 7, 1998: beta-test version 0.91.

The Macintosh does not allow PDB ID codes to be typed into the Browse slot. Therefore a separate slot has been provided for PDB ID's.
A bug which prevented items on the menu "Select previously loaded PDB file" from loading correctly on Macintoshes has (we hope) been fixed.
Water button now toggles water between hidden, dots, and spacefill. Bugs fixed: hetero button and water button now work in Comparator.
A bug which prevented the built-in Protein:DNA from being reported by the [?] button which reports "last file loaded" has been fixed.

October 4-5, 1998: beta-test version 0.9.

This is the first beta-test version, not yet an officially released version. It was offered to subscribers to the on October 4. On October 5, a bug in file-loading via Browse was fixed.