On Apr 27, 2009, at 9:39 AM, Elaine Meng wrote:
- draw lines between any pair of atoms, with control over color and
optional label of each line. You would do that by creating a simple
text file describing the lines and reading it in with Pseudobond Reader.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html
However, you would still have to calculate the violations yourself and
assign colors accordingly -- not nearly as automatic and convenient as
using NOESHOW.
Also, if the violation criteria were uniform, or only depended on heavy-atom element types or atom types, then it wouldn't be too hard to write a Python script to color the pseudobonds after they were read in. More sophisticated analysis that noeshow was capable of, such as exponential averaging across an ensemble of structures, would be some work though.
--Eric