Subject: Re: [nmr_sparky] distance constraints in 13C-edited spectra
From: Mandar T. Naik
Date: Nov 22 2:29 AM

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Thanks Eiso. The difference was very insignificant and can be overlooked.
-mandar

On Wednesday 22 November 2006 17:19, eiso wrote:
Mandar T. Naik wrote:
Hi Eiso,
I have one subquery on this, should one filter off the diagonal peaks
from the peaklist? I tried it both ways and got slightly different
results. Thanks in advance,

the diagonal peaks are filtered out by candid, so you can let them in.
if theres a real difference in the results (using the same random seed),
there should be a difference in the restraint list that caused it.
Im not sure but dont think the diagonal peaks are used for anything,
you could check the .noa files if theres a difference in the scores or
assignments.

note that difference random seed also give slightly different results,
sometimes larger than the rmsd.

Eiso

-mandar

--- In nmr_sparky@yahoogroups.com

mailto:nmr_sparky@yahoogroups.com , Betty Swanson betswanso@... wrote:
Dear SPARKY and CYANA users,

In SPARKY, for my protein the overall intensities of all cross
peaks in the 13C-edited NOESY spectra are medium or weak. Hence,
when I pool the peak lists from 15N-edited NOESY spectra and
13C-edited NOESY spectra and run CYANA, the upl file generated after
cycle7

do you mean CANDID or noeassign perhaps? CYANA can be run in many ways
if Im correct in CANDID the distances are calibrated with the assigned
distances
in the structure from the previous round. so if they are all medium
(what is
your definition of medium by the way?) that probably means that there
is not
much intensity difference in your NOEs. Is that the case? Is the
noe-mixing time
maybe too long?

contains larger distance constraints (~5.5 angstrom) for specific
cross peaks observed in the 13C-edited spectra. I expect
constraints for those cross peaks to be short (less that 2.5
angstrom) because they correspond to long range daa connectivity in
regions of protein corresponding to antiparallel betasheet. Why does
SPARKY display relatively weaker peak intensities for 13C-edited
NOESY spectra when compared to 15N-edited NOESY spectra

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