Subject: Re: [nmr_sparky] Re: Side chain assignment of small peptide.
From: Woonghee Lee
Date: Jan 4, 2018

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Dear Sohee,

There are a lot of factors that can influence the outcome quality of PINE. First thing you would like to check is peak lists. If you have a lot of noise peaks, you will not get good results. Also, make sure they align well with your backbone experiments. If you have sensitive C(CO)NH and H(CCO)NH, they provide better assignments than COSY and TOCSY combination. 

Best,
Woonghee

On Jan 4, 2018 11:48 PM, lavender1326@... [nmr_sparky] nmr_sparky@yahoogroups.com wrote:
 

Dear Woonghee,


Thanks for your reply.

I tried pine-sparky (command :ep) and got results.

backbone assignments were almost done and coincident with manual assignment. 
 
But results of side chain assignment is not good.

in case of HC(c)H-TOCSY and HC(c)H-COSY , only 7 of 300 peaks were assigned. 
and in case of CCH-TOCSY, it is better but  1/6 of peaks were assigned. 


why pine is not working well??

-Sohee