Modeling of CryoEM Map Workshop - Houston, Jan. 14-17, 2010
TCB Hands-on Workshop in Urbana
Tutorials
Below is a list of the tutorials used by TCBG instructors at
the CryoEM Map workshop. The were used in two tutorial sessions, "Introduction
into the Molecular Dynamics Flexible Fitting Method" and "Introduction into
Stereochemical Validation of Proteins and Nucleic Acids".
- Molecular Dynamics Flexible Fitting (MDFF) (html)
(pdf,
1.1M) (required tutorial files [.tar.gz,
29.7M] [.zip,
29.7M],
individual files)
This tutorial describes how to flexibly fit atomic
structures into density maps using the MDFF method. This
method can be used to obtain atomic models of
macromolecular complexes by combining X-ray structures and
cry-electron microscopy maps. Requires VMD and NAMD.
Tutorial works on Windows, Mac, and Unix/Linux platforms.
- Structure Check (pdf,
628k) (required tutorial files [.tar.gz,
762k] [.zip,
753k],
individual files)
This tutorial describes two VMD plugins that can be used
to detect and correct certain structure errors, namely
chirality and cis peptide bonds. The plugins can also be
used to prevent these errors from occuring in simulations
with NAMD. Requires VMD and NAMD. Tutorial works on
Windows, Mac, and Unix/Linux platforms.
