methyl group pseudo-atom treatment in CNS

adrs at chemistry.ucsc.edu adrs at chemistry.ucsc.edu
Fri Oct 9 13:41:31 EST 1998


I'm trying to figure out how to treat methyl groups when using the
anneal.inp input file for structure generation in CNS 0.4

Specifically, I have nOe ASSIGN statements in *.tbl files that use
pseudoatoms for the valine and leucine methyl groups in my sequence. 

Currently, I am adding no correction for the distance to the center of the
pseudoatom.  Is this the best approach, or should I be adding a correction?

Here is an example of my treatment, for a weak non-sequential interresidue
methyl-HN crosspeak from an 80ms noesy spectrum.  Residue 2 is a valine.

ASSign  ((resid 2 and name HG1#) OR (resid 2 and name HG2#))
        ( resid 7 and name HN)
        3.3000  1.7000  1.7000 

This is my all part of my first attempt to derive a structure from nOe data,
so any relevant advice would be appreciated.

I'm also interested to know how I should treat cross peaks involving methyls
in contrast to those involving just single protons in terms of the intensity
rankings.  These are for 2D spectra taken from a non-labeled sample (the
origin of this sample does not allow labeling).


--Joe

___________________________________________________________________________
D. Joe Anderson, Jr.		Dept. of Chemistry and Biochemistry
adrs at chemistry.ucsc.edu		UCSC, Santa Cruz, CA  95064
831/459-3390			http://elmo.ucsc.edu/~adrs/




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