Help, Index & Glossary for Protein Explorer (PE)

Released April 2001 (~100 terms); continuously updated, with major increments in June 2001 (~150 terms), August 2001 (~200 terms).

Can't find it? Please email suggestions for new entries in this index/glossary (or for additional information under existing entries) to Eric Martz. This index/glossary was begun with PE version 1.86 in April, 2001, and will require some time to evolve to reasonable completeness.

If the term you want is not in the alphabetic list below, try your browser's Edit, Find (in document) to see if it occurs anywhere below.

Protein Explorer (PE) is designed to be, as much as possible, self-explanatory. Beginners wishing an introductory overview should start with the QuickTour. When you don't know how to get the result you want, consult the Help, Index & Glossary for PE below -- it is always available within PE by clicking , or through a link in the Molecule Information Window, or a link on the FrontDoor. See also the Frequently Asked Questions (FAQ). Finally, the Tutorial provides a truly comprehensive tour.

Here are some Tips & Techniques for using PE effectively. Gale Rhodes (Univ. Southern Maine) has provided an excellent Glossary of Terms from Crystallography, NMR, and Homology Modeling.

Teachers: See the Lesson Plans and Assessment Questions.

Click on the first letter of the word you are looking for:

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Acknowledgements
Advanced Explorer
Advanced Explorer links to a number of powerful control pages and resources. Some of these require some familiarity with the command language. To get to Advanced Explorer:
Aliases, command.
Commands may be entered as abbreviations called "aliases". For more information, click the link Aliases below the message box.
Alignments.
The term "Alignment" can refer either to alignments of sequences, or of structures. For sequences, see MSA3D. Instructions are also available for making structural alignments.
Angles (simple, dihedral or torsion), reporting with mouse clicks.
In QuickViews, DISPLAY, Clicks, then check Report angles or Report dihedral (torsion) angles.
Animations.
Animations, movies, and morphs of conformational changes, thermal motion, etc. can be played in PE in a variety of renderings and color schemes, rotated for viewing from any perspective, and saved for playback outside of PE in Netscape or IE. For details and examples, click on the animated image of an EF hand near the top of the FrontDoor.
Assessment.
See Student Assessment of Learning Gains from Protein Explorer.
Atomic coordinate file
See PDB file. See also Axes, coordinate.
Axes, coordinate.
Each line in the PDB file that begins with "ATOM" gives the Cartesian coordinates for one atom -- its position in space. The origin of this coordinate system, and the directions of the axes, can be viewed by entering the command set axes on. (The background must be black).

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Back function.
Sorry -- see UnDo.
Backbone traces.
For an explanation, go to FirstView and click on backbone trace.
Bare Explorer or Comparator
"Bare" means that you enter Protein Explorer or Protein Comparator without pre-specifying a molecule in the link that starts PE. Bare Explorer/Comparator can be accessed from the FrontDoor.
Biology Workbench
The Biology Workbench is recommended for preparing multiple protein sequence alignments for use in PE's MSA3D. The MSA3D Tutorial (accessible from the MSA3D page within PE) includes step by step instructions for this use of Biology Workbench.
"Biomolecules"
Specific oligomers and complete virus capsids can be obtained with the link to Probable Quaternary Structures in the Molecule Information Window.
Bonds.
"Bonds" refers to bonds between atoms. Bonds may be either covalent (strong) or noncovalent (weak). The latter include van der Waals interactions, hydrogen bonds, and ionic bonds (such as salt bridges). PE attempts to show covalent bonds as rods between atoms, when the molecule is rendered in balls and sticks, or sticks. However, some strong bonds may not be shown as rods (especially involving metals, or between hetero atoms and protein or nucleic acid), or occasionally bond rods may be shown where only noncovalent bonds exist. Determination of the placement of bond rods is made by Chime. For details, see How Does Chime Determine Covalent Bonds?
Noncovalent bonds can be visualized with the Contacts option of the DISPLAY menu of QuickViews, or with the Noncovalent Bond Finder accessible in Advanced Explorer.
Browser, web.
The program used to retrieve hypertext information from the Internet and display it, commonly Internet Explorer or Netscape Navigator. PE works only inside a web browser, and requires a browser plugin called MDL Chime. PE tests the client's browser thoroughly for compatibility before starting a session.

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Chains
An introduction to chains is linked to FirstView. See also numbers for how to count the total number of chains. (WARNING: the "Number of Chains" reported in the message box is incorrect.
Charge of a protein.
You can see the charge of a protein at any pH by using EMBL's isoelectric point server.
Chime
Chime is a plugin that renders the image of the molecule. Protein Explorer is, in simple terms, a user interface to Chime, and is wholly dependent upon Chime. Chime works only on Windows and Macintosh, which limits PE to these platforms, although solutions are available for other platforms, including linux, Irix, etc. Chime is free, in part because it is built upon RasMol. Chime was developed by MDL Information Systems, Inc., largely by Tim Maffett, Bryan van Vliet, and Franklin Adler (none of whom remain at MDL), and by Jean Holt and others. Maffett deserves much of the credit for the design of Chime, for retaining the macromolecular capabilities of RasMol (of little interest to MDL), and for implementing many requests (not on MDL's agenda) made by Eric Martz. Unfortunately, Chime's source code is not made available by MDL. Chime is included in a commercial chemical database system, ISIS, which is the main revenue-generating product of MDL. Chime can be downloaded from MDL's Chime Site, where are also documentation and a discussion forum. See also the history of Chime.
Chime's Menu
Chime has a built-in menu, distinct from the QuickViews menus (and other menus) of PE. It is unusual to need Chime's menu, and it is rather poorly organized and contains no help. In the rare cases where it is useful, the QuickViews help frame will direct you to use it. To access Chime's menu, click on the MDL frank below and to the right of the molecule.

Some operations most easily accomplished with Chime's menu are spotting missing amino acids, listing the names of all ligand/hetero groups, and selecting all cases of one amino acid or nucleotide.

Citation of PE
See Literature about PE.
Classroom use of macromolecular visualization.
See Lesson Plans for Macromolecular Visualization.
Commands
Protein Explorer and Chime understand a superset of RasMol commands. Commands may be entered in the command slot in the frame at the lower left, above the message box. PE includes a document Using Commands, accessible from near the command input slot. There you will find links to the Command Reference Manuals.
Comparator
A alternate format of PE that provides side-by-side comparison of two molecules (PDB files) with all the same capabilities as the one-molecule version of PE. Rotations with the mouse can be synchronized. Comparator can be invoked bare, or by pre-specifying two molecules. Links and examples are on the FrontDoor.
Control page
The page at the upper left in the main (multiple-frame) PE window containing buttons, menus, and links that control the view of the molecule. Examples of control pages are FirstView, QuickViews, Advanced Explorer, MSA3D: Multiple Sequence Alignment Coloring, Cation-p Interactions/Salt Bridges.
Cookies
PE saves certain information between sessions on your computer. This information includes the most recently loaded molecules (for the Select previously loaded PDB file menu on the Load Molecules control page), preferences, The browser mechanism for saving such information is called "cookies" for obscure reasons. Here is more information about cookies and cookie safety.
Corey, Pauling, Koltun (CPK).
"CPK models" refers to physical, space-filling atomic models with atoms of van der Waals radii, developed in the pre-computer era. These CPK models also had a standard color scheme, similar to the "Element (CPK)" color scheme used in RasMol, inherited by Chime and hence by PE. One difference is that carbon was usually black in physical models, but is gray in PE. The CPK color scheme is incorporated into the DRuMS system of standard color schemes.
Counts of atoms, bonds, chains, residues, disulfide bonds, helices/strands/turns
See numbers.
CPK.
See Corey, Pauling, Koltin.
Crashing of Netscape or Internet Explorer.
If your browser stops responding ("freezes"), or "crashes", close all browser windows (on Macintosh, you must Quit from the application), restart the browser, and restart your PE session. This usually corrects problems. On rare occasions, you may need to reboot your computer to fix some strange behavior. See also Freezing and Tips & Techniques for using PE effectively. Netscape and Chime were developed simultaneously, and each has a few bugs that cause occasional problems. This is beyond our control, but it rarely causes a problem more than once or twice a day, even with PE sessions of several hours.
Crystal contacts
This information is available in the Molecule Information Window.
Crystallography, X-ray
See Nature of 3D Structural Data.
Cylinders,
as a cartoon rendering of alpha helices, are not available.

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DeepView.
DeepView, also known as SwissPDBViewer, is the best free modeling software package available. It can dock two molecules, structurally align two molecules, mutate PDB files, fill out unit cells and translate them using crystal symmetry, do homology models and energy minimization. The results can be saved as PDB files and explored in PE. DeepView and related resources can be found under freeware at molvisindex.org. PE includes instructions for using DeepView to construct crystal contacts. The best introductions to how to use DeepView are by Gale Rhodes.
Disorder.
See temperature value.
Distances between atoms, reporting with mouse clicks.
In QuickViews, DISPLAY, Clicks, then check Report distances (in Angstroms).
Disulfide bonds
An introduction to disulfide bonds and their rendering is available from a link at FirstView. For counts of disulfide bonds, see numbers.
Docking two molecules.
It is not possible to load multiple PDB files into Chime, nor move molecules relative to each other in a single Chime image. This can be simulated, laboriously, with animations of multiple-model ensembles in NMR format. Two molecules can be displayed side by side in Protein Comparator, and moved together in synchrony or independently. Two molecules can be aligned and displayed together, but cannot be moved relative to each other. It is possible to move molecules relative to each other in DeepView or Berkeley-RasMol.
Double molecule.
See multiple molecules.
Driscoll, Timothy
Author of the Script Recorder (under development) for Protein Explorer. Also authored the Chime shell and much of the content for the Biochemistry in 3D website for Lehninger's Principles of Biochemstry, and for Stryer's Biochemstry. See also DRuMS, the system of color schemes used in PE. Founder of MolVisions.Com.
DRuMS.
A system of standard color schemes for macromolecular visualization used in PE, documented by Tim Driscoll in collaboration with Frieda Reichsman. See the DRuMS Website.

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Entering a command.
Commands (or command aliases) may be typed in the slot that says "# Commands May Be Entered Here". Pressing the Enter key will then execute the command.
Evaluation.
See Assessment.
Expert mode
In the Preferences, if you check Expert, FirstView will not be shown unless requested, and in general less help and fewer alerts/warnings will be displayed.

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FAQ
Frequently Asked Questions, see PE's FAQ.
Fewer chains
Methods for eliminating some of the chains from your PDB file are explained in the link to Fewer or Single Chains in the Molecule Information Window.
FirstView
The control page titled FirstView describes the first view of a molecule offered by PE. To get to FirstView: FirstView introduces
Freezing of your computer
If your computer gets very slow while you are using PE, see if you have PE sessions (windows) in the background with spinning molecules. Spinning several molecules at once will make your computer very slow, even if you can't see them. Turn off unnecessary spinning, and close PE sessions you don't need. See also Crashing and Tips & Techniques for using PE effectively. Macintosh: Make sure you have given Netscape adequate memory -- see Troubleshooting.
FrontDoor
The first page you see when you go to www.proteinexplorer.org. Links that start PE by pre-specifying a molecule skip the FrontDoor. The FrontDoor provides numerous methods for entering PE, information about PE, and links to other Chime resources.

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Gaps.
See missing residues.

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Header (of PDB file)
The PDB file header is a block of text at the beginning of the PDB file that precedes the atomic coordinates. The header contains the original literature citations and sometimes remarks that are quite important. PE ignores most of the information in the header, but you can view the header from a link in the Molecule Information Window.
Hetero atoms
"Hetero" is a term defined in the PDB file format, and inherited by Chime and PE. It denotes all atoms that are not included in chains of protein or nucleic acid. Thus, hetero atoms include ligands, solvent, metal ions, and all carbohydrate moieties. Hetero atoms may or may not be covalently bound to chains of protein or nucleic acid. More information on "hetero atoms" is available at FirstView, and in QuickViews under SELECT Ligand, or SELECT Solvent.
History.
For the history of PE, see Purpose of the Protein Explorer, PE's Browser Testing mechanisms, RasMol, and Publications about PE.
Also available are a History of Visualization of Biological Macromolecules and the Earliest Solutions for Macromolecular Crystal Structures.
Homology modeling.
See Homology modeling for beginners.
HTML
HyperText Markup Language. The language that specifies how text will be formatted and displayed in a web browser, such as Netscape or Internet Explorer. PE is built with HTML and javascript.
Hydrogen atoms (and water)
Click on Water, and from there on more about hydrogen, starting from FirstView. Or here is a direct link to more about hydrogen. You can add hydrogen atoms to a molecule lacking them by using Gert Vriend's WHATIF WWW Interface. You can also use Chime itself to add hydrogen atoms to protein (but not nucleic acid, ligand, or solvent) -- but you cannot save them to a PDB file. Open Chime's menu, and select Options, Sprout Hydrogens. Next, you will need to select them (in QuickViews, SELECT Hydrogen, or SELECT All) and display them. Beware: Chime has been known to make some mistakes in where it puts the hydrogen atoms. Again, using Chime's menu for "File, Save molecule as" will save a PDB file but it will not include these hydrogens. Use WHATIF (above) if you need to save the hydrogen-decorated PDB file.
Hydrogen bonds.
At present, PE can display only two subsets of hydrogen bonds: protein backbone-to-backbone hbonds within chains (but not between chains), and Watson-Crick hbonds between DNA base pairs. These can be shown in QuickViews: DISPLAY Hbonds, where further information will be shown automatically. PE presently has no built-in routines to show hbonds between backbone and sidechain, backbone and water, sidechain and sidechain, sidechain and water, protein and ligand, protein and nucleic acid, non-canonical hbonds in DNA or RNA, etc. However, manual methods are available to show arbitrary bonds.

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Internet Explorer
Prior to 2002, PE worked only in the Netscape browser. In version 1.91 Beta, PE was adapted to work in either browser, with the help of Paul Pillot and Jean-Philippe Demers (see Protein Explorer's Browser Testing for Microsoft's Internet Explorer and Netscape Communicator and Protein Explorer's Implementation in Microsoft's Internet Explorer). See also Tips & Techniques for IE-specific tips. (These IE-specific tips display only if you are using IE).
Irix
Protein Explorer works well in a Microsoft Windows window on SGI/Irix supported by Citrix Metaframe.
Isoelectric point of a protein.
The isoelectric point, or pI, is the pH at which a protein has zero net charge. When the pH is higher than the isoelectric point, the protein has negative charge, and when lower, positive charge. You can calculate the iselectric point of your protein easily using on-line resources.
  1. First, get the one-letter amino acid sequence of your protein. Open the Molecule Information Window and click on the link to Structure Explorer from RCSB. There click on the link (at the left) Sequence Details, and on that page, click on Download all chains in FASTA format. Block the sequence of the chain of interest (excluding the comment line beginning >) and copy it to the clipboard.
  2. Second, go to the EMBL WWW Gateway to Isoelectric Point Service, paste your sequence in the box, and press the button.
  3. Warning: the sequence you paste in must be in UPPER CASE one letter code. If you paste in a lower case sequence, you'll get pI = 6.014999, which is for the backbone only, because it doesn't recognize lower case amino acids!

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javascript
The programming language with which PE is built, along with HTML. Javascript is a programming language that works only within the web browser. Javascript is interpreted by the browser. Basically, it adds programming capability to HTML documents. Javascript should not be confused with java, a general-purpose, cross-platform programming language. In PE, javascript controls Chime by sending it commands. PE comprises over 40,000 lines of HTML plus javascript.
javascript error(s)
Javascript errors should not occur when running PE, unless you do not have Chime configured properly. In that case, you will never see any molecule in PE, and you need to consult Troubleshooting.
If Protein Explorer did show you a molecule, and then during the session a javascript error occurred, the most likely reason is that Netscape or Chime has become unstable or unreliable. This may happen occasionally while using Protein Explorer and it is usually not your fault (but see Tips and Techniques for using PE Effectively). The solution is simply to close all your browser windows (on Macintosh, use the File menu to Quit), wait a few seconds, and then restart your browser and begin a new session of PE. If that doesn't prevent the javascript error, try rebooting your computer. If you get a javascript error reproducibly after the same action, despite restarting your browser and rebooting, you have found a bug that should be reported. Diagnosis is best done in Netscape rather than Internet Explorer. Type "javascript:" (including the colon) in the location slot of Netscape, and copy the error report into an email. Describe in detail what version of PE you are using, and what actions induced the error. Send the report to yours truly.

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Labels, adding with mouse clicks.
In QuickViews, DISPLAY, Clicks, then check Display labels on atoms.
Lesson plans.
See Lesson Plans for Macromolecular Visualization.
Ligand.
In general, "ligand" usually means a small molecule specifically bound to a macromolecule by noncovalent bonds. In Chime and PE, "ligand" has a somewhat different definition: all hetero atoms that are not solvent. "Ligand" in this PE sense may be noncovalently or covalently bound to non-hetero atoms, namely chains of protein or nucleic acid. For example, both a noncovalently-bound enzyme inhibitor, and an asparagine-linked (covalently bound) carbohydrate adduct qualify as "ligands" in PE. On the other hand, a single standard nucleotide (A, C, G, T, or U) bound to a protein noncovalently does not fall under the term "ligand" as defined within Chime and thus PE, even though it would be considered "ligand" in the more usual, general sense. In QuickViews, pressing the [Ligand] button shows a short definition and explanation.

You can conveniently list the names of all ligand groups present in your structure with Chime's Menu: Select, Residue. In the resulting submenu, following the 20 amino acids, are listed all ligand (hetero) group names (limited to 1-3 characters in length).

Limitations.
The following limitations exist in Protein Explorer:
linux
Protein Explorer works well in a Windows subsystem running under linux.
Literature
See Literature about PE.
Load Molecules
The Load Molecules control page allows molecules to be loaded from PDB files saved to the local disk (press the [Browse] button), from the Protein Data Bank via Internet if you know the PDB identification code, or from a menu of the most recently loaded molecules. To get to the Load Molecules control page, from the FrontDoor, enter Bare Explorer, and it will appear automatically. Alternatively, from within a PE session, if you are at QuickViews or Advanced Explorer, click on the link Different Molecule; or from anyplace in PE, enter .l (period plus lower case "L", no space between) in the command entry slot.

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Maffett, Tim.
See Chime.
Martz, Eric.
Author of PE. From 1971-1997, an immunologist and cell biologist. See his personal page. Self-taught programmer, who (prior to his involvement in molecular visualization beginning in 1995) wrote the first personal bibliographic management system (Bibliofile, 1981-1991, later known as Document Management System for Citations, no longer on the market), and MFI (1992-1995), a freeware data analysis program for flow cytometry.
Menus
In PE, the menu system is QuickViews. There is also a (rarely needed) menu built into Chime.
MEP
See molecular electrostatic potential.
Message Box.
A white box in the lower left frame. When you press buttons or use menus in the control page, commands are generated automatically by PE and sent to Chime. These commands are shown in the message box, along with other messages from PE or Chime, such as the selected atom count after a "select" command.
Missing amino acids.
Here is an easy way to find out whether all 20 amino acids are present in your structure. Using Chime's menu, Select, Residue. On the resulting submenu, all 20 amino acids are listed. If any are not present, they are gray instead of black.
Missing residues.
Some residues present in the crystal may be missing, leaving "gaps". Perhaps they were not assigned coordinates because their disorder (or "temperature") was too high in the crystal. This is often the case for the ends of chains, or extended surface loops. For more information about possible reasons for gaps or missing residues, open the Molecule Information Window, and click on either Sequences or Seq3D. This will open a sequence display window, where you will find links to Help about missing residues.
Modeling, molecular.
"Molecular modeling" means changing the positions or bonding relationships of atoms, by homology modeling, energy minimization, molecular dynamics, etc. It is distinct from "molecular visualization" which, strictly speaking, means looking at a structure without modifying it. The best freeware package for macromolecular modeling is DeepView. See also mutation.
Model quality
See Quality, Model.
Molecule name
Available in the Molecule Information Window.
Molecular electrostatic potential
"Molecular electrostatic potential" (MEP) refers to the distribution of electrostatic charges (including partial charges) in a molecule. Most often, it is displayed on a solvent-accessible surface of the molecule, as a color scheme (red negative, blue positive, following CPK). Advanced Explorer has a link to Surfaces, where you can apply various MEP color schemes. However, if you plan to use MEP very often, see the Comparision of MEP Renderings for a better solution.
Molecule Information Window
Opened with the Mol Info link available in every control page.
Monitor lines, showing distances between atoms, inserting with mouse clicks.
In QuickViews, DISPLAY, Clicks, then check Display monitor lines between pairs of atoms.
Morphs.
See Animations.
Mouse controls.
See
Movies.
See Animations.
MSA3D
"Multiple Sequence Alignment 3D", a feature within PE that can color a 3D protein to show regions of conservation or mutation based on a multiple protein sequence alignment. For an introduction to MSA3D, click on the small protein image labeled "Color by multiple sequence alignment" at the upper left of the FrontDoor. MSA3D is accessed from a link in Advanced Explorer.
Multiple models (in a single PDB file).
Multiple models (molecules) can be included in a single PDB file, and displayed in PE, if they are in NMR format. QuickViews displays only the first model. To see other models, from Advanced Explorer, click on the link to NMR Models/Animation. PE can play the models as a movie, or examine them one at a time, or in selected subsets.
Multiple molecules (multiple PDB files).
See Protein Comparator and docking.
Multiple Sequence Alignment
See MSA3D.
Mutation.
"Mutation" means changing one or more amino acids or nucleotides in a protein or nucleic acid chain. Mutation of a 3D model is modeling, and hence not within the capabilities of PE. However, it is quite easy to mutate a protein 3D model (PDB file) using DeepView, and then explore the result in PE. See Mutating Residues in PDB Files.

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Name of molecule
Available in the Molecule Information Window.
Netscape Communicator/Navigator
Netscape is the web browser that defined the plugin, and LiveConnect, a protocol for communication between the browser and the plugin. Chime was developed for Netscape at a time when Netscape was used by the majority of people (1995-8). PE was developed in Netscape, and from its first release (version 0.9 in October 1998) through 2001, PE worked only in Netscape. Because Internet Explorer (IE) became the predominant browser by the new millenium, PE was adapted to work in IE late in 2001, with the help of Paul Pillot and Jean-Philippe Demers (see Protein Explorer's Browser Testing for Microsoft's Internet Explorer and Netscape Communicator).
New features in PE
See version history of PE.
NMR
PE can display and facilitate analysis of ensembles of models from NMR experiments. See multiple models and animations. For an introduction to nuclear magnetic resonance, see Nature of 3D Structural Data. See also the NMR format for PDB files.
NMR format for PDB files.
Multiple models can be manipulated independently in PE if they are in the NMR PDB format. This is standard PDB format plus special records (lines) in the PDB file to delimit the models. The ATOM records for each model must begin with a line "MODEL N", where N is the model number (beginning with one for the first model and going up), and end with a line "ENDMDL". The N in "MODEL N" should line up with the element symbol column. For a small example, see 1TOS, a 3-model PDB file for a 10 amino acid peptide.
Nuclear Magnetic Resonance
See NMR.
Numbers (total counts) of atoms, bonds (covalent and hydrogen), chains, residues, disulfide bonds, helices/strands/turns
Click the link Show counts in the Molecule Information Window to display the total counts for the molecule currently loaded.

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Oligomers
Specific oligomers and complete virus capsids can be obtained with the link to Probable Quaternary Structures in the Molecule Information Window.

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Papers about PE
See Literature about PE.
PDB
PDB stands for Protein Data Bank, the sole international repository of all published three-dimensional macromolecular structure data. "PDB terms" include:
Pedagogy.
See lesson plans.
pI
See isoelectric point.
Powerpoint.
A still snapshot can be copied from PE and pasted directly into a PowerPoint slide. See saving images. If you want to rotate the image during the presentation, the best solution is to run both PE and PowerPoint at the same time. When you get to the point in your presentation where you want to show and rotate the molecule, simply pop the PE window in front. To return to PowerPoint, pop its window in front.
Preferences
Click the link Preferences below the message box to see the preference settings. Preferences are remembered between PE sessions. They are specific to the computer upon which they are set (and to the person, if multiple personal profiles have been created in the browser). Preferences are saved as cookies.
Presentations in PE and Chime.
Support for making presentations in PE is under development. Examples demonstrating the concept of presentations in PE are available. Also under development is a command script recorder that will work within PE's QuickViews to capture the commands generated by menus and buttons, and assist in saving them to a disk file.
Detailed instructions are available for authoring presentations in Chime (not in PE), including a template that includes all required HTML and javascript. This older (pre-PE) method requires learning the RasMol command language.
Printing publication-quality images.
Molecular images in PE are rendered by Chime, using code developed for RasMol. In writing RasMol, Roger Sayle made an excellent compromise between image quality and speed of interactive rotation of the image. As a result, the images are less satisfactory for publication (see limitations). (Most published macromolecular images are generated with MolScript, see molvisindex.org under freeware.) Often, however, satisfactory images can be obtained for publication by using the largest screen resolution available (e.g. 1600 x 1200 pixels) together with PE, and then saving the image.
Project folders.
Project folders are a feature for advanced users who wish to write command scripts. Project folders (disk directories designated to PE) contain PDB (.pdb) and script (.spt) files that can be loaded and executed in PE. For more information, click the Set Project Folder link below the message box.
Protein Data Bank
See PDB.
Probable Quaternary Structures
Specific oligomers and complete virus capsids can be obtained with the link to Probable Quaternary Structures in the Molecule Information Window.
Protein Explorer (PE)
Freeware for visual exploration of macromolecular 3D structure. A user interface that makes the power of Chime accessible to students, educators, and occasional users. Easier to use, and much more powerful than RasMol. Independently described as an "impressive integrated knowledge base". Accessible at www.proteinexplorer.org. See also PE's history.
Publications about PE
See Literature about PE.
Publication-quality images, printing.
See Printing.

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Quality of the model
The models published in PDB files for X-ray crystallography vary widely in quality, and rarely they are grossly incorrect. Some useful information on model quality, including the Ramachandran plots, can be obtained from PDBReports, linked to Model Quality in the Molecule Information Window. For examples of published errors, see Kleywegt, 2000, and Kleywegt and Brunger, 1996.
Quaternary Structures
Specific oligomers and complete virus capsids can be obtained with the link to Probable Quaternary Structures in the Molecule Information Window.
QuickTour
The QuickTour is the best way for beginners to become familiar with PE. It is available from a link on the FrontDoor, or from links on the FirstView page.
QuickViews
The QuickViews menu system is the heart of the user-friendly exploration power in PE. QuickViews enables you to explore extensively without learning any of Chime's command language. To get to QuickViews:
Quotations about PE
See Literature about PE.

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Ramachandran plots
See Quality of the model.
Range of residues, selecting, coloring, etc.
To select a range of residues from the sequence, open the Molecule Information Window, and there, open Seq3D. In the Seq3D window, check Show & select range, then click on the first and last residues of the desired range. The residues are now selected, and you can return to QuickViews to change their DISPLAY or COLOR scheme. (If you wish to select more than one range at a time, in Seq3D, check Accumulate selections.)
RasMol
The molecular graphics in PE come from RasMol, a brilliant, stand-alone molecular visualization program written by Roger A. Sayle (see his personal history of RasMol). RasMol is freeware and open-source, thanks to the generosity of its author. Because of that, the RasMol-derivative Chime is free, and because of that (and thanks to the National Science Foundation), PE is free. RasMol is used by millions of people. RasMol and extensive documentation are available from the RasMol Home Page. PE is much easier to use, and more powerful than RasMol.
Reichsman, Frieda
Suggested some important user-friendliness design features of PE and its Tutorial. Author of content for several major topics in Biochemistry in 3D for Lehninger's Principles of Biochemistry. Founder of Molecules In Motion where some additional high-quality Chime tutorials are available.
Resolution.
X-ray crystallographic models are characterized by a "Resolution" value, which can be obtained in REMARK 2 in the PDB file header (available in the Molecule Information Window). (Do not confuse "Resolution" with "R Value" or "Free R".) Small numeric values for resolution mean small uncertainty, hence good resolution; larger values mean poor resolution. For example, 5.0 Å is rather poor resolution for a protein, 2.5 Å resolves more atomic positions with greater certainty, and 1.2 Å is high resolution for a protein, where hydrogen atoms can begin to be discerned. On average, the uncertainty of the position of an atom is roughly one fifth to one tenth of the resolution for high-quality data (R-factor 0.20 or less, succinctly explained in Rhodes). However, uncertainty typically varies from region to region of the model, and is reflected in the temperature value assigned to each atom.
In NMR results, uncertainty in the position of an atom is represented by the range of positions of that atom in the ensemble of models.
Rhodes, Gale
Author of Crystallography Made Crystal Clear, second edition, 1999, a very readable introduction highly recommended for beginners interested in crystallography. See Gale Rhodes' personal website, which has links to many excellent tutorials on molecular visualization and modeling, especially with the use of DeepView.
Rotation troubleshooting.
Dragging on the molecule with the mouse should rotate it. If the molecule fails to rotate, but instead slides without rotating, Netscape and Chime have become corrupted. This is not your fault. The solution is simply to close all Netscape windows (or on Macintosh, File, Quit Netscape). Then restart Netscape and start a new PE session. We hope this doesn't happen to you when you're projecting PE to illustrate a talk -- but it has occasionally happened to us in that situation. Just smile, explain that PE, Netscape and Chime are all under development and hence are not totally bug-free, and proceed by quitting and restarting Netscape. It won't happen again in the same talk, usually.

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Saving images from PE.
Still "snapshot" images are easy to save from PE. Click on the MDL below the molecular image to pop up Chime's menu. Click on Edit, Copy. This copies the image to the clipboard. You can now paste it into any graphics program (e.g. Windows Paint), PowerPoint, or Word (Edit, Paste Special, Bitmap). From a graphics program, an image saved in .jpg (jpeg) format can be displayed directly in a web page since web browsers understand this format.
If you want to save the state of your PE session, so you can return to the same image of the molecule easily later, see scripts, saving.
Sayle, Roger,
see RasMol.
Scripts, of commands.
Chime has an extensive command language, a superset of RasMol's command language. PE's menus and buttons generate commands and send them to Chime (using javascript). The commands can be seen in PE's message box. Scripts of commands can be saved in a plain text file, and run in PE. See the link Set Project Folder beneath PE's message box for details on running command scripts in PE.
Scripts, saving.
Command scripts can be saved automatically, then played back in order to restore the currently displayed image. At present, the only method to do this is one built into Chime. Click on the MDL frank to the lower right of the molecular image, thereby opening Chime's menu, then Edit, Copy Chime Script. This places the script on the clipboard, from which it can be pasted into any text editor (WordPad in Windows, or BBEdit on Macintosh). The script must be saved as plain text (but with a filename ending .spt) in order to run in Chime. These scripts are unnecessarily long and may take an unnecessarily long time to produce the image -- see Shortening Scripts Saved from RasMol or Chime. These scripts are generated by a mechanism inherited from RasMol which contains a few bugs, and which does not know about surfaces. Hence, they will not generate surfaces, and commands must be inserted manually to restore surfaces.
In order to overcome the limitations of scripts saved automatically from Chime, a script recorder is under development. See Presentations in PE.
The best way to play back a command script file is to set a project folder.
Selection methods
Selected atom count
Chime's rendering (display) and coloring commands always work on the currently selected atoms. Atoms can be selected with the QuickViews SELECT menu, or with commands. After each selection operation, the number of atoms selected is reported in the message box. It is also displayed in a slot below the image of the molecule (except in Comparator).
Seq3D
Seq3D is a clickable sequence display that can be used to highlight the locations of particular amino acids in the 3D display. It can also be used to select arbitrary amino acids from the sequence listing (using the option to "Accumulate Selections"), or to highlight and select a range of amino acids (using the option "Show and select range", then clicking on the ends of the range). Seq3D is accessed from the Molecule Information Window. For a tour of how to use it, see the QuickTour including the section "Beyond the QuickTour".
Sequences
The sequence(s) of the chain(s) of the currently loaded molecule are available in the Molecule Information Window. There, click Sequences for an annotated listing of the sequences, or click Seq3D for a shorter listing that you can click to select and locate residues or ranges of residues.
SGI
Protein Explorer works well in a Microsoft Windows window on SGI/Irix supported by Citrix Metaframe.
Show counts
(An option in the Molecule Information Window.) See Numbers.
Simplified PE?
Some educators have inquired about a "simplified" PE. While PE itself has not been simplified, something in that vein has been provided in MolUSc, but it is available only in French (any volunteers to translate it?). MolUSc is a technically well-documented visualization interface, integrated knowledge base offered in PE.
Single chains
Methods for eliminating some, or all but one, of the chains from your PDB file are explained in the link to Fewer or Single Chains in the Molecule Information Window.
Snapshots
It is easy to save a snapshot of your molecule. See Saving images from PE.
Solvent.
In general, of course, the major solvent involved both in protein crystallography and NMR is water. However, in Chime and therefore in PE, the term "solvent" includes, in addition to water, some nonmacromolecular solutes, namely sulfate and phosphate ions, that may be incidentally bound to protein. In PE, all hetero atoms are divided into ligand and solvent. For more information about the definition of "solvent" see "predefined sets" in the RasMol Reference Manual.
Surfaces
Chime (and hence Protein Explorer) can display surfaces of selected atoms. These are solvent-accessible surfaces that represent the contact path of a sphere rolled around the outside of the cluster of selected atoms. The probe sphere is, by default, 1.4 Å in radius, the size of a water molecule. Surfaces are used in QuickViews DISPLAY Contacts, or DISPLAY Surface. In Advanced Explorer, the Surfaces page enables generation of multiple surfaces concurrently. Here, a variety of color schemes can be applied, including molecular electrostatic potential or molecular lipophilicity potential. Also, the probe radius and spacing, the algorithms used for potential calculations, and the coloring for potentials are adjustable.
Synch.
The [Synch] button appears only in Protein Comparator. Moreover, it appears only in Windows; this capability was not implemented in Chime 2 for the Macintosh. When synchronization is turned on with this button, and one molecule is rotated with the mouse, the other molecule will rotate synchronously. In fact, all mouse-controlled operations will be synchronized.

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Teaching molecular structure.
See Lesson Plans for Macromolecular Visualization.
Temperature value (disorder).
Uncertainty in the positions of atoms increases with "disorder" in the protein crystal. Some regions of the molecule may have higher average disorder, and others lower average disorder. Typically, the ends of chains have higher average disorder, and hence their positions are less certain than are residues in the core of a tightly packed domain, where disorder is less.
    "Disorder" has two components. First, some regions of the molecule may adopt different conformations in different copies of the molecule, each molecule's conformation being stable. Second, some regions of every copy of the molecule may be subject to thermal motion, meaning vibration about the rest position (Rhodes). Thermal motion is minimized when the crystal is frozen with liquid nitrogen while being irradiated.
    In the PDB format, each atom is given not only X, Y, and Z Cartesian coordinates, but two additional values immediately following called "occupancy" and "temperature factor" (also known as the "isotropic B value"). If the end of a chain adopts either of two stable positions with equal probability, each position has 50% occupancy. The temperature factor is provided to quantitate the level of thermal motion. However, these two components of disorder cannot be distinguished with crystal diffraction data alone. Therefore, the occupancy is often given as 1.0 (100%), while the degree of "blur" in the electron density map, representing both components of disorder, is reported in the temperature value.
    PE's QuickViews COLOR menu offers a Temperature color scheme, in which the range of temperatures is assigned a spectral sequence from blue (low temperature, higher certainty) to red (higher temperature, higher uncertainty). Often the very ends of chains, or surface loops, may be so disordered as to prevent assigning an positions at all, leading to missing residues.
Total counts of atoms, bonds, chains, residues, disulfide bonds, helices/strands/turns
See numbers.
Troubleshooting
Tutorial
PE includes an extensive Tutorial.
Two molecules at once.
See Protein Comparator and docking.

 

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UnDo.
There is, unfortunately, no "undo" capability. A plan for such a capability has been formulated for implementation in a future release. See also limitations.
Unit cell, crystallographic.
This is the smallest portion of a crystal that, when replicated in three dimensions, makes up the entire crystal. It can be viewed by entering the command set unitcell on. (The background must be black). See Crystal contacts and Axes, coordinate.

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Version history of PE
PE includes the history of all released versions, which lists the new features added in each version.
Virus capsids
Complete virus capsids can be obtained with the link to Probable Quaternary Structures in the Molecule Information Window, provided you have the appropriate virus capsid PDB file loaded.
Visualization, molecular.
Strictly speaking, "molecular visualization" means looking at a structure without changing it, that is, without performing molecular modeling.

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Workshops
Workshops and workshop syllabi to train students, faculty, and researchers in the uses of PE and related resources are available.

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X-ray crystallography
See Nature of 3D Structural Data.

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References Cited