Thank you Ben for the useful information.
On Tue, Apr 19, 2011 at 12:40 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
> 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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Thanks,
Naveen Samala
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Received on Tue Apr 19 2011 - 11:30:03 PDT
