Subject: Re: [nmr_sparky] distance constraints in 13C-edited spectra
From: Mandar T. Naik
Date: Nov 21 5:35 PM

Previous: 299 Next: 303

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,

-mandar

--- In

href=mailto:nmr_sparky@yahoogroups.comnmr_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