Molecular Visualization in Biochemistry Education
Kinemage workshop


in association with Mississippi Academy of Sciences
14 February 2003

This page links the resources available for download associated with this workshop. The PDB files are linked and sourced here for the convenience of the workshop participants, the Protein Data Bank is the ultimate source for these files.

Organization of this page follows the major sections of this day-long workshop:
Set-Up and Install Software
Walkthrough of Program Features
3D Literacy
Advanced Features
Other resources will be handed out and or made available for download during the workshop.

     Set-Up

Install most recent versions of Mage, Prekin and Probe software.
Check-out and troubleshoot installation problems.

computer OS or platformclick to go to download page
PC-Windows, Linux,
SGI, and MacOS9
no Probe available for Mac OS9
Mage download page

Prekin download page

Probe download page
NB: Probe software not available for MacOS9
Mac OSX Mage, Prekin, and Probe
All three from one page

Note that the programs are precompiled and are thus computer-platform specific. Kinemage files (also called ".kins") are text files and are not computer-platform specific. Well, sort of. There is a difference in end-of-line characters: Macs use ASCII 13 (\r, <CR>), *nix boxes use ASCII 10 (\n, <LF>), and PCs use both. The only effect having the wrong EOL code may have is reading the file in an unsophisticated editor. All text files are supplied with *nix (ASCII 10) line-feeds. Also note that depending upon your browser set-up, some of the items, particularly the kinemage text files, will display rather than download. If so, force the download by "right-clicking", "control-clicking", or some-such browser trick.

     Walkthrough of Program Features

An introduction to the functionality of Mage, Prekin, Probe and another -- Reduce.
Intro to MolProbity - our web server running these programs.

PDB files for this section:
7AHL.pdb  ||  1CGL.pdb  ||  5CPA.pdb  ||  3CPA.pdb  ||  1STP.pdb  ||  1EHZ.pdb

Other files for this section:
Typical use of Mage-Probe to generate all-atom contact analysis:  HTML  ||  PDF

     3-D Literacy Workshop

The versatility of Mage: teaching, testing, feedback, analysis

Kinemages and PDBs for this section:
3Dlit4atst.kin  ||  HbondPractice.kin  ||  1lmb6_85Hbox.kin  ||  1lmb6_85H.pdb

Other files for this section:
3D Literacy kinemage text:  HTML  ||  PDF
H-bond test kinemage text:  HTML  ||  PDF

     Advanced Features

More examples of Mage versatility:

Kinemages and PDBs for this section:
aladipeptsimplified.kin  ||  1GVV.pdb  ||  1HIH.pdb  ||  1UBQ.pdb  ||  1ubqH13-15-33-71-73.kip