Subject: Re: backbone assignment experiments
From: ethernet3399
Date: Sep 29, 2005

Previous: 3

Hi sandra,
You are welcome!
A suggestion: you can read the sparkys manual, Automated Protein
Backbone Assignment part. In this part, the author says we can
acquire 8 triple resonance spectra(2D N15HSQC is needed too):

HNCO, HN(CA)CO; HNCACB, CBCA(CO)NH; HNCA, CA(CO)NH; HNHA, HA(CO)NH

Sometimes maybe we do need all the 8(4 pairs) spectra, I assigned a
104 residue protein backbone with the following spectra:
N15HSQC
HNCACB
CBCA(CO)NH
HNCO
HN(CA)CO
HNHA

I think at least the 5 spectra(N15HSQC, HNCACB, CBCA(CO)NH, HNCO,
HN(CA)CO ) are absolutely needed.

Your tocsy spectra can help the side chain assignment, and the noesy
spectra assignment is the last step to extract the noe peak intensity,
which as input for structure calculation.

Your friend,
Tieying Zhang
at SIBS

--- In nmr_sparky@yahoogroups.com , sandramike_05
sandramike_05@y... wrote:

Hi,

Nice to know that we have a NMR group for sparky. Im a new user
learning the NMR assignment. Im doing the assignment of a 13KDa
protein. My questions is can you suggest me a list to NMR experiments
needed to have a complete backbone NMR assignment. I already have

HNCA, HNCOCA, HNCACB, CBCACONH, HHBHACONH, HCCCH-TOCSY, 15N-1H, HSQC-
NOESY & TOCSY.

Thanks,

SM

--- In nmr_sparky@yahoogroups.com , ethernet3399 tyzhang@s... wrote:
because the hcch_tocsy spectrums different H-H record order, it has
to change the axis order which conversion from NMRPipe to Sparky, the
post before this have presented a solution, but not the best one.
Here
it goes:

which conversion of the hcch_tocsy spectrum, use the following
command:

pipe2ucsf -213 pipefile ucsffile

instead the usual one:

pipe2ucsf pipefile ucsffile

then, this little problem can be easily get rid of.