Subject: Re: [nmr_sparky] distance constraints in 13C-edited spectra
From: eiso
Date: Nov 22 1:19 AM
Previous: 301 Next: 304
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
Messages in this topic