Can't find it? Please email suggestions for new entries
in this index/glossary (or for additional information under
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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.
Protein Explorer (PE) is designed to be, as much as possible,
self-explanatory.
Beginners wishing an introductory overview should first do the
QuickTour.
The present
Help, Index & Glossary for PE
is always available
within PE by clicking
, or
through a link in the
Molecule Information Window.
The
Tutorial provides a comprehensive tour.
Here are some
Tips & Techniques for using PE effectively.
Click on the first letter of the word you are looking for:
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- 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:
- from FirstView:
click on Explore More!, which takes you to
QuickViews.
- from QuickViews:
click on the link to Advanced Explorer below the cluster
of buttons.
- from anywhere else, click Back.
- from anywhere, enter the
command .x ("x" preceded by a period).
- Atomic coordinate file
- See PDB file.
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- 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.
- "Biomolecules"
- 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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- 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 window is incorrect.
- 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.,
and unfortunately its 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.
- 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 window.
PE includes a document
Using Commands, accessible
from
near the
command input slot.
- 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.
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.
- Counts of
atoms, bonds, chains, residues,
disulfide bonds, helices/strands/turns
- See numbers.
- Crashing of Netscape.
- If your browser stops responding, or "crashes", close all browser
windows
(on Macintosh, you must Quit from the application),
restart Netscape, and restart your 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.
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- Disulfide bonds
- An introduction to disulfide bonds and their rendering
is available from a link at FirstView. For
counts of disulfide bonds, see numbers.
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- 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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- 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:
- You'll arrive at FirstView automatically whenever you start PE,
unless you have checked
Expert
in
Preferences.
- from QuickViews,
if you just want to see the FirstView page without
changing the current view of the molecule,
click on FirstView: Info Only.
- from QuickViews,
if you want to reset the view of the molecule
to the default "first view"
click on FirstView: Reset View.
- from Advanced Explorer,
if you just want to see the FirstView page without
changing the current view of the molecule,
click on QuickViews, and there, click on FirstView:
Info Only.
- from Advanced Explorer,
if you want to reset the view of the molecule
to the default "first view"
click on Reset.
- from other
control pages, press the Back button to return
to Advanced Explorer (then see above).
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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- 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, a term defined in the PDB file format,
denotes atoms that are not included in chains of protein
or DNA. Thus, hetero atoms include ligands, solvent, metal ions,
and all carbohydrate moieties. Information on "hetero" is
available at FirstView, and in QuickViews
under SELECT Ligand, or SELECT Solvent.
- 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 (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.
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- Internet Explorer
- Microsoft's Internet Explorer web browser (IE) is not compatible with
Protein Explorer
because it employs features of
Chime that are supported only in
Netscape
(notably LiveConnect). Efforts are in progress to make a version of
PE that is compatible with IE.
- Irix
- Protein Explorer works well in a
Microsoft Windows window
on SGI/Irix supported by Citrix Metaframe.
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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 Netscape browser,
and to some extent, within the Internet Explorer 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.
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- linux
- Protein Explorer works well in a
Windows subsystem
running under linux.
- 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.
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- Message Window
- 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 window, along with other messages from PE or Chime, such as the
selected atom count after a "select" command.
- Model quality
- See
Quality, Model.
- Molecule name
- Available in the Molecule Information Window.
- Molecule Information Window
- Gotten with the button
available in every
control page.
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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).
Because
PE depends upon LiveConnect, it cannot
presently work in
Internet Explorer.
- NMR
-
For an introduction to nuclear magnetic resonance, see
Nature of 3D Structural Data.
- Nuclear Magnetic Resonance
-
See
Nature of 3D Structural Data.
-
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.
- Atoms:
The first number reported in the message window
is the number of atoms in protein or nucleic acid chains.
The number in (parentheses) is the number of hetero
atoms. The sum of these two is the total number of atoms.
Remember that for most PDB files resulting from X-ray crystallography,
you should multiply by two to estimate the total atoms including
hydrogens.
See also selected atom count.
- Bonds (covalent):
Covalent bonds are usually determined by Chime. (CONECT records in the PDB file [see PDB file format] are ignored, except
for certain special cases.) Chime assigns covalent bonds
to any two atoms having a distance from each other of
less than 1.9 Å. Here is
detailed information about bonds.
- Chains:
The "Number of Chains" reported in the message window is
INCORRECT!. The best way to count the number of
chains is to count them in the Sequences display.
See also chains.
- Hydrogen bonds:
See hydrogen bonds.
- Residues:
Residues are called "groups" in Chime. The first number listed after
"Number of Groups" is the number of amino acid plus nucleotide residues.
The number in (parentheses) is the number of hetero
residues.
- Disulfide bonds:Again, Chime assigns disulfide bonds
based on proximities of cysteine sulfur atoms.
(SSBOND records in the PDB file are ignored.)
The "Number of Bridges" is correct for single-model (most X-ray) files,
but might be incorrect (too high) if multiple positions (coordinate sets) are given
for some cysteine sidechains. It is incorrect for NMR ensembles of models,
because of a bug that assigns bonds between, as well as within, models.
See also disulfide bonds.
- Helices/Strands/Turns:
For information on the methods used by Chime to assign secondary structure,
in QuickViews do COLOR Structure, and read the
help in the middle frame.
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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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- PDB
- PDB stands for
Protein Data Bank, the sole international repository
of all published three-dimensional macromolecular structure data.
"PDB terms" include:
- PDB identification code: Each molecular structure published
at the PDB is assigned a unique four-character code. The first character
must be a numeral; the last three characters can be either letters
or numerals. Examples: 1d66 (Gal 4 complexed to DNA), 1hho (oxyhemoglobin),
1bl8 (potassium channel).
- PDB file: The data file that specifies the positions in
space of every atom in a molecule. The generic name for such a file
is an atomic coordinate file. If the file is in PDB format,
the filename should end with .pdb to be widely recognizable,
including by servers.
- PDB format: One of several file formats for
atomic coordinate files. The PDB format is old, ambiguous, and
inadequate, but is still the most widely used format because all
relevant software can read it. An newer and more flexible
alternative format, agreed upon
by the International Union of Crystallographers, is mmCIF
(macromolecular crystallographic information format). Although mmCIF
is offered by the PDB, it is not in wide use. Chime
cannot read mmCIF, but RasMol (version 2.7
and later) can.
Here is a
short overview of the PDB format.
The official format specification is available from the
Protein Data Bank.
- 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.
- 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.
Accessible at
www.proteinexplorer.org.
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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
simply 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.
-
Kleywegt, G. J. 2000. Validation of protein crystal structures.
Acta. Crystallogr. D. Biol. Crystallogr. 56:249-265.
-
Kleywegt, G. J., and R. J. Read. 1997. Not your average density.
Structure. 5:1557-1569.
-
Kleywegt, G. J., and A. T. Brunger. 1996. Checking your imagination:
applications of the free R value. Structure. 4:897-904.
-
Kleywegt, G. J., and T. A. Jones. 1996. Phi/psi-chology: Ramachandran
revisited. Structure. 4:1395-1400.
- Quaternary Structures
- Specific oligomers and complete virus capsids
can be obtained with the link to
Probable Quaternary Structures in the
Molecule Information Window.
- 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:
- from FirstView:
click on Explore More!.
- from Advanced Explorer:
click on QuickViews!.
- from anywhere else, click on Back to return to
Advanced Explorer.
- from anywhere, enter the command .q
("q" preceded by a period).
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- Ramachandran plots
- See Quality of the model.
- RasMol
- The molecular graphics in PE come from RasMol,
a brilliant, stand-alone molecular visualization program written by Roger A. Sayle.
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.
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- Selection methods
- Choose SELECT, >HELP< in QuickViews.
See also Selected atom count.
- 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 window. It is also displayed in a slot below the image of the
molecule (except in Comparator).
- 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.
- 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.
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- Total counts of
atoms, bonds, chains, residues,
disulfide bonds, helices/strands/turns
- See numbers.
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- Virus capsids
- Complete virus capsids and other specific oligomers
can be obtained with the link to
Probable Quaternary Structures in the
Molecule Information Window.
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- X-ray crystallography
-
See
Nature of 3D Structural Data.
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