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BCH222 :: How To Make Your Own Kinemages

Graphics Assignment

The graphics assignment is to do the Tutorial--How To Make Kinemages, using KiNG, and email your resulting kinemage file to the course TA. This should give you examples of most of the kinds of things you might need to do in making the kinemages for your class project. The various programs, documentation, and PDB files mentioned are available from the BCH222 site.

This tutorial lets you practice by using KiNG to construct a multi-part kinemage file to illustrate the structural features of ricin (PDB file 2AAI). These instructions lead you through most of the authoring functions for making your own kinemages, including stylistic suggestions on how to choose views, colors, button layouts, ribbons, superpositions, etc. in ways that will help communicate your 3-D ideas effectively. The more specialized functions of rotatable bonds, mutations, and all-atom contacts are referred to a separate later exercise called All-Atom Contacts.

To understand the structure and format of the .kin text files you are producing, and to look up specific features of the kinemage format, see the kinemage file format description document (pdf). If you want to construct a kinemage feature you have seen in a previous example, use a word-processor to look at how it was done in that file and construct yours by analogy.

Reading on KiNG:

V.B. Chen, I.W. Davis and D.C. Richardson (2009) KiNG (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program Protein Sci. 18:2403-2409 doi: 10.1002/pro.250 (open access). PMID: 19768809

Optional background reading

On kinemages:

D.C. Richardson & J.S. Richardson (1992) The kinemage: a tool for scientific communication Protein Sci. 1:3-9. PMID: 1304880

On ricin:

PDF E. Rutenber, …, J.D. Robertus (1991) Crystallographic refinement of ricin to 2.5 Å, PROTEINS: Structure, Function, and Genetics 10:240, 251, 260 doi: 10.1002/prot.340100308