Subject: Assignment distances for methyls
From: Tom Goddard
Date: Jul 14, 2010

Greetings Tom,

Is there a way to make arbitrary atom assignments that would match
with the pdb atoms so that one can see the distances in this panel? For
example, the pdb file has coordinates for all 3 protons of a methyl
group but I only have one peak assigned to the group. The possible
assignment shows with the offsets, but no distances (I assume because
the name doesnt match exactly). I have tried using * or # in the
assignment but neither work.

Jessica

Hi Jessica,

The Sparky assignment distance dialog isnt smart enough to match
atom names using patterns (e.g. HB*), it only handles exact matches.

http://www.cgl.ucsf.edu/home/sparky/manual/extensions.html#AssignmentDistance

Sometimes there are creative ways around these limitations. For
instance you could make 3 PDB files with methyl atom 1 in the first PDB
renamed to match the sparky resonance name, in the second pdb file,
rename just methyl atom 2 (for all methyls) to the Sparky resonance
name, .... Then open all 3 pdb files in the assignment distances dialog
so you can see distances for all 3 methyls protons. Might work.

Tom