Hi
I am a PhD student at the University of Southampton and am new to NMR and am currently going through the CCPN version 2
Iam trying to assign a 99 amino acid protein (beta 2 microglobulin) and have a couple of minor issues and not sure where to go next with the assignment!
I have attached 3 screenshots:
screenshot 5 shows a message 'spin system set up has produced warnings' - does this mean a ca/cb has been assigned to more than one spin system?
screenshot 4 is from when I am assigning the own ca/cb and this shows that in the carbon part, there are several other ca's other than the current spin system (7), does this mean that that ca has already been assigned to another spin system?
the last screenshot shows the 'assignment reliability after I have performed the automated protein backbone assignment. Have you any advice as to how I can 'improve' the assignment reliability prediction scores??
thanks very much for your help
SAM HILL
________________________________________
From: Hill S.D.
Sent: 26 November 2008 13:44
To: [log in to unmask]
Subject: FW: CCPN 2
Hi
I am a PhD student at the University of Southampton and am new to NMR and am currently going through the CCPN version 2
Iam trying to assign a 99 amino acid protein (beta 2 microglobulin) and have a couple of minor issues and not sure where to go next with the assignment!
I have attached 3 screenshots:
screenshot 5 shows a message 'spin system set up has produced warnings' - does this mean a ca/cb has been assigned to more than one spin system?
screenshot 4 is from when I am assigning the own ca/cb and this shows that in the carbon part, there are several other ca's other than the current spin system (7), does this mean that that ca has already been assigned to another spin system?
the last screenshot shows the 'assignment reliability after I have performed the automated protein backbone assignment. Have you any advice as to how I can 'improve' the assignment reliability prediction scores??
thanks very much for your help
SAM HILL
________________________________________
From: Hill S.D.
Sent: 26 November 2008 12:40
To: Vicky Higman
Subject: RE: CCPN 2
Dear Vicky
I hope you are well
I have attached 3 screenshots:
screenshot 5 shows a message 'spin system set up has produced warnings'.
screenshot 4 is from when I am assigning the own ca/cb and this shows that in the carbon part, there are several other ca's other than the current spin system (7)
the last screenshot shows the 'assignment reliability after I have performed the automated protein backbone assignment. Have you any advice as to how I can 'improve' the assignment reliability prediction scores??
thanks very much and all the best
Sam Hill
________________________________________
From: Vicky Higman [[log in to unmask]]
Sent: 25 November 2008 16:31
To: Hill S.D.
Subject: Re: CCPN 2
Dear Sam,
I'm not entirely sure what you mean with the 'automated assignment' - do you mean the 'link sequential spin systems' pop-up? I think version 2 of Analysis also has a proper automatic assignment routine, though I haven't looked into that myself yet - I'm only gradually migrating from version 1 to version 2.
I am also not quite sure what you mean with the fact that they are 'unassigned to an amino acid' - do you mean an 'amino acid type' or a 'spin system'? It might be easiest if you send me a screen shot describing what you are having problems with. But in principle you should always be able to do an assignment or specify a new spin system type in the assignment pop-up - place the mouse over the peak and press 'a'.
Otherwise perhaps Stuart Findlow in Southampton might be able to help you - I think he has been using CCPN Analysis, too.
Best wishes,
Vicky
2008/11/25 Hill S.D. <[log in to unmask]<mailto:[log in to unmask]>>
Dear Vicky
I am at the University of Southampton, UK and am new to NMR but am going through the CCPN version 2 by your notes.
After I have assigned the own ca/cb and have searched for matching peak pairs in the CBCACONH, I have run an automated assignment and there are a few peaks that are unassigned to an amino acid, I was just wondering if you have any advice as to how I can make these peaks assigned to an amino acid?
Thanks very much for you help
Sam Hill
--
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Dr. Victoria A. Higman
Leibniz-Institut fuer Molekulare Pharmakologie (FMP)
NMR-Supported Structural Biology
Robert-Roessle-Str. 10
13125 Berlin
Germany
and
School of Chemistry
University of Bristol
Bristol BS8 1TS
United Kingdom
Phone: +49-30-94793-238
E-mail: [log in to unmask]<mailto:[log in to unmask]> (or [log in to unmask]<mailto:[log in to unmask]>)
http://www.protein-nmr.org.uk
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