[Chimera-users] Contact/clash detection for HETATMs

Jonathan Magasin jmagasin23 at yahoo.com
Mon Feb 4 13:06:22 PST 2008


I'm trying to use the clashes/contacts tool to explore
valid phi/psi angles for L- and D-Ala (as part of a
homework assignment; developing a Ramachandran plot
for each).  The tool worked great for L-Ala but does
not report any contacts for D-Ala.  (For each, I've
snipped just the relevant sections out of a larger
PDB.  I'm using default params for collision
detection, with detection calculated for any

The difference in the PDB's for L-Ala and D-Ala is
that the latter are in HETATM records.  I did include
the CONNECT info (to explicitly tell Chimera how
HETATMs bond) but that did not help.

Perhaps there's something else I must include, or some
modification I can make to the HETATMS (element
labeling?) so that collision detection will work as
with peptides?  Or is this a known limitation?  (Is
there a list of known limitations?  I'm a new user.) 
I'm not 

Note that the distance tool works for D-Ala.  If I can
get collision detection to work, it take much less

Thanks in advance.


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