Advanced Protein Explorer Workshop
Weizmann Institute of Science
June 25, 2000 - Eric Martz (firstname.lastname@example.org)
The agenda for this workshop will be informal, and will adapt to the
interests of the participants. Collaborations are invited that use
Protein Explorer to display information about macromolecular structure,
particularly information which may be the result of your research.
To start Protein Explorer, go to inn-prot.weizmann.ac.il, click
on the Proteomics button, then on INN-PROT (first link on the page), then
on Software, then scroll down and click on Protein Explorer.
Possible topics for the workshop include:
To find this page on the web, go to the RasMol Classic Main Page
(www.umass.edu/microbio/rasmol) and click on Education, then
Software training, then look under the list of workshops.
- Overview or Protein Explorer's QuickViews menus and Seq3D
for selection, display, and coloring.
- Sequence irregularities (insertions and non-physical gaps, 1igt;
physical gaps, 2ace; microheterogeneity, 1cbn).
- Protein Explorer's preferences: expert mode.
- Contact Surfaces for an overview of the noncovalent bonds
between any two moieties. For a start, use QuickViews' DISPLAY
menu, selecting Contacts. Then, under Advanced Explorer's Contact Surfaces
page are many more options.
- The NonCovalent Bond Finder: a press of the [Find]
button displays the atoms closest to any moiety. Additional
clicks on [Find] step out in 0.1 Angstrom shells. Clicking on a
found atom displays the whole residue to which it belongs.
Distances from putatively bonded atoms can be displayed. To keep
the image simple, hydrogen bonds and hydrophobic interactions can
be dealt with in separate scans.
- MSA3D: Coloring a molecule according to a multiple protein
- Obtaining a multiple protein sequence alignment at
the Biology Workbench.
- Searching for structurally similar proteins, without
reference to sequence: CE (Combinatorial Extension, Shindyalov &
Bourne), Vector Alignment Search Tool (US National Center for
- Surfaces colored by electrostatic potential or
molecular lipophilicity potential.
- Structural alignment of two or more molecules. The
CE site will align any two protein chains quickly and easily (but
hetero atoms are discarded). Swiss PDB Viewer can align anything
(one or more than one chains), selecting any subset of atoms for
the alignment (other atoms following), and retaining hetero
atoms. The results can be saved as a PDB file. It will need
manual editing to separate models with MODEL [N] and ENDMDL
records so that Protein Explorer can distinguish the models.
- Morphing: making movies of protein conformational changes.
and scripts for Chime.