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).
This document is updated frequently, more often than is the downloadable
version of PE. If you can't find something, check on-line
at proteinexplorer.org,
for the very latest version of this document.
Can't find it? Please email suggestions for new entries in this index/glossary (or for additional information under existing entries) to Eric Martz. My goal is that the term you first think of should be here -- at least as a cross reference to another entry!
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.
PE's FrontDoor
has a wealth of introductory information.
Beginners wishing an introductory overview should start with the
1-Hour Tour.
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.
|
Ala A Alanine
Arg R aRginine Asn N asparagiNe Asp D "asparDic" (aspartic) acid Cys C Cysteine |
Gln Q "Quetamine" (glutamine)
Glu E "gluEtamic" (glutamic) acid Gly G Glycine His H Histidine Ile I Isoleucine |
Leu L Leucine
Lys K "liKesine" (lysine) Met M Methionine Phe F "Fenylalanine" (phenylalanine) Pro P Proline |
Ser S Serine
Thr T Threonine Trp W tWyptophan (tryptophan) Tyr Y tYrosine Val V Valine |
Animations.
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.
near the
command input slot. There you will find links to the Command
Reference Manuals.
PE simplifies typing commands with its
command aliases.
|
within a protein. |
Jeffrey categorizes hbonds with donor-acceptor distances of 2.2-2.5 Å as "strong, mostly covalent", 2.5-3.2 Å as "moderate, mostly electrostatic", 3.2-4.0 Å as "weak, electrostatic" (page 12). Energies are given as 40-14, 15-4, and <4 kcal/mol respectively. Most hbonds in proteins are in the moderate category, strong hbonds requiring moieties or conditions that are rare within proteins. The hydrogen atoms in moderate hbonds often do not lie on the straight line connecting the donor to acceptor, so donor-acceptor distance slightly underestimates the length of the hbone (Jeffrey, p. 14). The mean donor-acceptor distances in protein secondary structure elements are close to 3.0 Å, as are those between bases in Watson-Crick pairing (Jeffrey, pp. 191, 200). Since many PDB files lack hydrogen atoms, the presence of an energetically significant hydrogen bond can be inferred when a probable donor and acceptor are within 3.5 Å of each other. PE's DISPLAY Contacts defines "likely noncovalently bonded" oxygens and nitrogens (shown as balls) as those within 3.5 Å of other oxygens and nitrogens.
At present, PE can display as rods connecting atoms 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.
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).
At present, the only method to save a command script 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.
The best way to play back a command script file is to
set a project folder.
In order to overcome the limitations of scripts saved automatically
from Chime, a script recorder is under development.
See Presentations in PE.
