Hi Andrew,
This is the way you do it, using the dipo command.
methyl group: divide measured coupling by -3 and use carbons instead of the
protons.
e.g. for an Ala methyl, you would use the CA-CB vector in the selection. For
Ile delta methyl,
the selection would be CG1-CD1.
methyle group: you could do one of two things:
(a) sum option. e.g. for a beta methylene you would have
(assign (resid x and name cb) (resid x and name hb#) sum of
couplings -ve error +ve error
(b) the better way is to use the sum-diff option. Same selection as in
(a) but now you enter:
assign (resid x and name cb) ((resid x and name hb1) or (resid x and
name hb2))
coupling1 -error +error
coupling2 -error + error
The order is irrelevant because the program will automatically figure out
which coupling is used with
which proton from the sum and differences of the couplings. (This is the
same method that is also
used for chemical shift restraints for methylene protons; check out the
publications section
on my web site and you can pull out the relevant publications, which are
cited in the Xplor-NIH J. Magn. Reson paper).
Good luck.
Marius
G. Marius Clore, MD, PhD
Chief, protein NMR Section
Laboratory of Chemical Physics
Bldg 5, Room B1-30I
NIDDK, National Institutes of Health
Bethesda, MD 20892-0520
Tel: (301) 496 0782
Fax: (301) 496 0825
e-mail: [email protected]
web: http://spin.niddk.nih.gov/clore
> ----------
> From: Andrew Bennett
> Reply To: Andrew Bennett
> Sent: Thursday, December 11, 2003 3:14 PM
> To: [email protected]
> Cc: [email protected]
> Subject: [Xplor-nih] Question about Setting Up CH2 and CH3 RDC
> Constraints
>
>
> December 11, 2003
>
> Dear Colleagues,
>
> I wanted to ask you an xplor-nih question. By the way, the program rocks
> and I got a lot out of the previous help threads. Thanks for providing
> all of this stuff.
>
> I have some CH, CH2, CH3 rdc couplings from constant time c13hsqc
> experiments and I was wondering how one can set up the xplor calculations
> with methylene and methyl data as described conceptually in "Measurement
> of Dipolar Couplings for methylene and methy sites in weakly oriented
> macromolecules," Ottiger et al, JMR 134:365 (1998). The paper talks about
> setting up methyl and methylene constraints in xplor to the average sums
> of the CH vectors but I am not sure how to implement that in xplor-nih.
> Possibly you have an example tbl file or other supportive information or
> relevant examples.
>
> I would appreciate any information you may have about how to set this up
> and any examples.
>
> Thanks very much for your assistance.
>
> Sincerely,
> Andrew Bennett, M.D., Ph.D.
> Gerhard Wagner Laboratory
> Harvard Medical School
> [email protected] (that's a zero in the middle)
>
>
>
>
>
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