Hi again,
On 19/4/2011, at 1:31 p.m., Ben Roberts wrote:
>> 2. In section 16.10.6 Side Chain Model , what do the terms bd, ag, tr,
>> and 87.0 mean in the following line of code?
>> addFragment terminal/CH3 bd /NAME/CLR/HD1-1/.CB. ag /NAME/CLR/HD1-1/.CG. tr
>> /NAME/CLR/HD1-1/.ND1 87.0
>
> They stand for "bond", "angle" and "torsion" respectively. The bond, angle and torsion are used to position the new fragment (a methyl group, in this case) relative to the three atoms provided (in this case, the beta carbon, gamma carbon and delta nitrogen of the histidine residue).
I also forgot to mention, the "87.0" is the size of the torsion angle to use when adding the methyl group. The bond and angle don't need to be specified; I guess the program gets their value from tables somewhere.
Ben
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Received on Tue Apr 19 2011 - 11:00:04 PDT
