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Re: [nmrpipe] Please help me to calculate the difference in Comp. Chem. shift

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  • Sridevi Ramakrishnan
    I am glad to receive the answers from the members. Thank you very much for your kind help. Regards, Sridevi. ...
    Message 1 of 10 , Jun 30 6:28 PM
      I am glad to receive the answers from the members.
      Thank you very much for your kind help.

      Regards,
      Sridevi.

      --- Andy Vendel <acvendel@...> wrote:

      > If you are going look at changes in chemical shift
      > between two spectra by combining the 1H and 15N
      > chemical shifts it is best to weight the 15N
      > chemical
      > shift values using this equation:
      >
      > delta_av= sqrrt{(delta_HN)^2+(delta_N/5)^2}
      >
      > Campbell & Lumb 2002, Radhakrishnan et al 1999,
      > Grzesiek et al 1996
      >
      > Cheers,
      >
      > Andy
      >
      > --- Patrik Lundström <patrik.lundstrom@...>
      > wrote:
      >
      > > This little script should do the trick assuming
      > you
      > > have peaklists from nmrDraw with proton chemical
      > > shifts in column 6 and 15N in column 7. In my
      > > example the peaklists are called test.tab and
      > > test2.tab. I just loop over the asignments, grep
      > out
      > > the shifts and calculate the difference.
      > >
      > > / Patrik
      > >
      > >
      > > #!/bin/csh
      > >
      > > foreach name (F89 F92 F141 Y99 Y138)
      > > set Hppm1 = `grep $name test.tab | awk '{print
      > $6}'`
      > > set Nppm1 = `grep $name test.tab | awk '{print
      > $7}'`
      > > set Hppm2 = `grep $name test2.tab | awk '{print
      > > $6}'`
      > > set Nppm2 = `grep $name test2.tab | awk '{print
      > > $7}'`
      > >
      > > set Hdiff = `awk 'BEGIN{ print
      > '$Hppm1'-'$Hppm2'}'`
      > > set Ndiff = `awk 'BEGIN{ print
      > '$Nppm1'-'$Nppm2'}'`
      > >
      > > echo $name $Hdiff $Ndiff
      > >
      > > end
      > >
      > >
      > > ----- Original Message -----
      > > From: Sridevi Ramakrishnan
      > > <sri_cecri2004@...>
      > > Date: Tuesday, June 27, 2006 8:25 pm
      > > Subject: [nmrpipe] Please help me to calculate the
      > > difference in Comp. Chem. shift
      > >
      > > >
      > > > Dear all,
      > > >
      > > > I am a begginer in NMR field. Could you please
      > > write
      > > > me how to calculate the difference in compound
      > > > chemical shift of amide proton and nitrogen
      > > between
      > > > two protein conformations? Is there any program
      > to
      > > > calculate this if we load the peaklist of two
      > > 15N-HSQC
      > > > spectra?
      > > >
      > > > Regards,
      > > > Sridevi,
      > > > Graduate Student,
      > > > Auburn University.
      > > >
      > > >
      > > >
      > > >
      > >
      >
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    • Mandar T. Naik
      Hi A slightly different weighing factor for N is advocated by Kay et.al. in Nat. Struct. Biol. 2001 Sep; 8(9):756-60. delta_dtot = SQRT [(dHNWHN)2 + (dNWN)2 +
      Message 2 of 10 , Jun 30 6:34 PM

        Hi
        A slightly different weighing factor for N is advocated by Kay et.al. in Nat. Struct. Biol. 2001 Sep; 8(9):756-60.

        delta_dtot = SQRT [(dHNWHN)2 + (dNWN)2 + (dCOWCO)2 + (dCAWCA)2]

        Here WHN =1, WN = 0.154, WCA = 0.276 and WCO = 0.341

        Text from the paper: "The weight factors were determined from the ratio of the average variances of the 1HN shifts and the chemical shifts of nucleus type i as observed for the 20 common amino acids in proteins using the BioMagResBank chemical shift database."

        I see use of both equations in literature and this might actually result in very trivial change though some authoritative comment is expected for consistency.


        Best regards
        -mandar




        ----- Original Message -----
        From: Andy Vendel
        To: nmrpipe@yahoogroups.com
        Sent: Saturday, July 01, 2006 2:20 AM
        Subject: Re: [nmrpipe] Please help me to calculate the difference in Comp. Chem. shift


        If you are going look at changes in chemical shift
        between two spectra by combining the 1H and 15N
        chemical shifts it is best to weight the 15N chemical
        shift values using this equation:

        delta_av= sqrrt{(delta_HN)^2+(delta_N/5)^2}

        Campbell & Lumb 2002, Radhakrishnan et al 1999,
        Grzesiek et al 1996

        Cheers,

        Andy

        --- Patrik Lundström <patrik.lundstrom@...>
        wrote:

        > This little script should do the trick assuming you
        > have peaklists from nmrDraw with proton chemical
        > shifts in column 6 and 15N in column 7. In my
        > example the peaklists are called test.tab and
        > test2.tab. I just loop over the asignments, grep out
        > the shifts and calculate the difference.
        >
        > / Patrik
        >
        >
        > #!/bin/csh
        >
        > foreach name (F89 F92 F141 Y99 Y138)
        > set Hppm1 = `grep $name test.tab | awk '{print $6}'`
        > set Nppm1 = `grep $name test.tab | awk '{print $7}'`
        > set Hppm2 = `grep $name test2.tab | awk '{print
        > $6}'`
        > set Nppm2 = `grep $name test2.tab | awk '{print
        > $7}'`
        >
        > set Hdiff = `awk 'BEGIN{ print '$Hppm1'-'$Hppm2'}'`
        > set Ndiff = `awk 'BEGIN{ print '$Nppm1'-'$Nppm2'}'`
        >
        > echo $name $Hdiff $Ndiff
        >
        > end
        >
        >
        > ----- Original Message -----
        > From: Sridevi Ramakrishnan
        > <sri_cecri2004@...>
        > Date: Tuesday, June 27, 2006 8:25 pm
        > Subject: [nmrpipe] Please help me to calculate the
        > difference in Comp. Chem. shift
        >
        > >
        > > Dear all,
        > >
        > > I am a begginer in NMR field. Could you please
        > write
        > > me how to calculate the difference in compound
        > > chemical shift of amide proton and nitrogen
        > between
        > > two protein conformations? Is there any program to
        > > calculate this if we load the peaklist of two
        > 15N-HSQC
        > > spectra?
        > >
        > > Regards,
        > > Sridevi,
        > > Graduate Student,
        > > Auburn University.
        > >
        > >
        > >
        > >
        >
        __________________________________________________________
        > > Yahoo! India Answers: Share what you know. Learn
        > something new
        > > http://in.answers.yahoo.com/
        > >
        > >
        > >
        > >
        > >
        > > ------------------------ Yahoo! Groups Sponsor
        > --------------------
        > > ~-->
        > > Yahoo! Groups gets a make over. See the new email
        > design.
        > >
        >
        http://us.click.yahoo.com/XISQkA/lOaOAA/yQLSAA/cEYolB/TM
        > >
        >
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