[MMTK] Reading a coordinated CYS from a PDB file

Jose Borreguero borreguero at gmail.com
Mon Oct 13 20:55:23 UTC 2008

Dear MMTK users,
I have four CYS coordinated to a Fe atom in a PDB file which I want to read.
Because of the coordination, all the CYS lack the H_gamma. When I read the
pdb file:

*universe = InfiniteUniverse()*
*conf = PDBConfiguration(mypdb)
t = Trajectory(universe, nc_file, "w", "hello", block_size = 1)*

I see that  *universe._atoms* contains the H_gamma atoms for the CYS. So, my
question is: does my "universe" contain four extra ghost atoms (one H_gamma
for each of my four CYS) ?

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