Hi Wayne,
many thanks for the prompt help.
I am forwarding the e-mail conversation to the ccpnmr mailing list for the sake
of documentation.
with regards,
K.Aswani Kumar
------------------------------- Original Message -------------------------------
Subject: Re: Distance Restraints from 2D H,H NOESY spectrum; problem with
multiplets (fwd)
From: "Wayne Boucher" <[log in to unmask]>
Date: Fri, May 27, 2011 3:11 pm
To: "kancherla Aswani Kumar" <[log in to unmask]>
--------------------------------------------------------------------------------
---------- Forwarded message ----------
Date: Fri, 27 May 2011 10:37:29 +0100 (BST)
From: Tim Stevens <[log in to unmask]>
To: Wayne Boucher <[log in to unmask]>
Subject: Re: Distance Restraints from 2D H,
H NOESY spectrum; problem with multiplets (fwd)
Cool. I've added the macro to the repository on the web site and have posted it
in the v2.2.1 updates (to go in python/ccpnmr/analysis/macros/).
T.
> ---------- Forwarded message ----------
> Date: Fri, 27 May 2011 11:33:15 +0530 (IST)
> From: kancherla Aswani Kumar <[log in to unmask]>
> To: Wayne Boucher <[log in to unmask]>
> Subject: Re: Distance Restraints from 2D H,
> H NOESY spectrum; problem with multiplets (fwd)
>
> Hi Wayne and Tim,
> The Macro "MakeDecoupledPeakList.py" worked fine. I used the macro to get a
> new
> peak-list and then made the distance restraints from that peak-list for using
> in
> structure calculation. There was no problem in using the new peak-list for
> making distance restraints.
>
> As an internal check, I compared the number of unique distance restraints
> between backbone nuclei in the restraint-list made from the original noesy
> peak-list and the in the restraint list made from the new decoupled
> peak-list.
> The number remained same indicating that nothing unexpected/undesirable has
> happened during the new processing steps.
>
> Many thanks for the prompt help.
>
> with regards,
> Aswani Kumar K
>
>
>
>> A modified version from Tim.
>>
>> Wayne
>>
>> ---------- Forwarded message ----------
>> Date: Wed, 25 May 2011 12:59:15 +0100 (BST)
>> From: Tim Stevens <[log in to unmask]>
>> To: Wayne Boucher <[log in to unmask]>
>> Subject: Re: Distance Restraints from 2D H,
>> H NOESY spectrum; problem with multiplets (fwd)
>>
>>
>> Probably doesn't like the mention of it being synthetic, so I have scrubbed
>> that bit.
>>
>> Attached,
>>
>> T.
>>
>>>
>>> ---------- Forwarded message ----------
>>> Date: Wed, 25 May 2011 16:55:52 +0530 (IST)
>>> From: kancherla Aswani Kumar <[log in to unmask]>
>>> To: Wayne Boucher <[log in to unmask]>
>>> Subject: Re: Distance Restraints from 2D H,
>>> H NOESY spectrum; problem with multiplets (fwd)
>>>
>>> Hello Wayne,
>>> Many thanks for the prompt reply and the macro.
>>>
>>> I have downloaded the Macro, added it and I have run it. The macro worked
>>> perfectly fine and a new synthetic peak list is created. I checked the
>>> position
>>> of the synthetic cross-peaks and they are fine.
>>>
>>> However, when i try to make a distance restraint file using the pop-up,
>>> "M::Structure::Make_Distance_Restraints", the scroll down menu in the
>>> pop-up
>>> doesn't show me the option of newly created peak-list. I have made sure
>>> that
>>> I
>>> activated the new peak-list using the "M::Peak::Peak_Lists menu."
>>>
>>> In essence, I could use the Macro "MakeDecoupledPeakList.py" to generate a
>>> decoupled peak list but I am unable to use the peak-list to make distance
>>> restraints. I couldn't think of any reason why the menu
>>> "M::Structure::Make_Distance_Restraints" is not recognizing the newly
>>> generated
>>> peak_list.
>>>
>>>
>>> Thanking you,
>>>
>>> with regards,
>>>
>>> K.Aswani Kumar
>>>
>>> Graduate Student
>>> Molecular Biophysics Unit
>>> Indian Institute of Science
>>> Bangalore-560012
>>> India
>>>
>>>
>>>> Hello,
>>>>
>>>> See the message below from Tim, and the attached Python script.
>>>>
>>>> Wayne
>>>>
>>>> ---------- Forwarded message ----------
>>>> Date: Wed, 25 May 2011 11:10:18 +0100 (BST)
>>>> From: Tim Stevens <[log in to unmask]>
>>>> To: Wayne Boucher <[log in to unmask]>
>>>> Subject: Re: Distance Restraints from 2D H,
>>>> H NOESY spectrum; problem with multiplets (fwd)
>>>>
>>>>
>>>> OK, I suggest Aswani tries the attached macro. If it works OK I will post
>>>> on
>>>> the web site.
>>>>
>>>> This asks for the peak list which contains the multiplets and creates a
>>>> separate sibling list with 'decoupled' peaks.
>>>>
>>>> Each new peak is created by combining multiplet peaks that have exactly
>>>> the
>>>> same assignments (there is no provision for mixed ambiguity in only part
>>>> of
>>>> a
>>>> multiplet). The new peak intensities are the summation of the multiplet
>>>> peaks
>>>> and the new positions are the multiplet means.
>>>>
>>>> The new peak list should make better distance restraints. Naturally if the
>>>> original peak assignments change the 'decoupled' list should be recreated.
>>>>
>>>> T.
>>>>
>>>>>
>>>>> Using decoupled spectra is recommended and proper handling of couplings
>>>>> had
>>>>> been put back to v3.
>>>>>
>>>>> I suppose I could script something to merge the peak intensities and
>>>>> positions (of identically assigned peaks) to give a 'decoupled' list...
>>>>>
>>>>> T.
>>>>>
>>>>>
>>>>>> ---------- Forwarded message ----------
>>>>>> Date: Tue, 24 May 2011 12:08:55 +0100
>>>>>> From: Aswani Kumar K <[log in to unmask]>
>>>>>> Reply-To: CcpNmr software mailing list <[log in to unmask]>
>>>>>> To: [log in to unmask]
>>>>>> Subject: Distance Restraints from 2D H,H NOESY spectrum; problem with
>>>>>> multiplets
>>>>>>
>>>>>> Hello Analysis Team/Users,
>>>>>>
>>>>>> I have a 2D H,H NOESY spectrum for a 44 residue long peptide (~4.5 kDa).
>>>>>> The
>>>>>> scalar couplings are manifested in the directly acquired dimension of
>>>>>> the
>>>>>> spectrum and most of the noesy correlations are observed as multiplets.
>>>>>> For
>>>>>> example the intra residue noesy correlation between amide proton and
>>>>>> alpha
>>>>>> proton of a given residue (say 11Cys) is split into two in the directly
>>>>>> acquired dimension (so it has two cross-peaks/cross-hairs on the peak).
>>>>>> During the sequence specific assignment, I have assigned all the
>>>>>> cross-hairs
>>>>>> of a given correlation peak with the appropriate resonances (say 11Cys H
>>>>>> and
>>>>>> 11Cys HA). The multiplicity is even higher for the protons of the side
>>>>>> chains.
>>>>>>
>>>>>> When I make the distance restraints using the noesy spectrum peak
>>>>>> volumes/intensities, analysis returns multiple distance restraints for
>>>>>> the
>>>>>> same pair of nuclei whenever the noesy correlation peak between the two
>>>>>> nuclei is split. For example the restraint file has two distance
>>>>>> restraints
>>>>>> for 11Cys H and 11Cys HA (probably one restraint for each cross-hair).
>>>>>> Moreover, the peak volume seems to be divided amongst all the
>>>>>> cross-hairs
>>>>>> and consequently the distance over-estimated. For example the
>>>>>> upper-limit
>>>>>> for the 11Cys H-HA distance is reported as 6 Angstrom.
>>>>>>
>>>>>> How can we make analysis return one distance restraint per each pair of
>>>>>> nuclei? Is it possible to get one average distance restraint for each
>>>>>> pair
>>>>>> of nuclei without actually merging the multiplets? If the cross-hairs
>>>>>> need
>>>>>> to be merged, what is the best way to do it?
>>>>>>
>>>>>> Or is there a completely different and better way out of this situation?
>>>>>>
>>>>>> Thanking you in advance,
>>>>>>
>>>>>> K.Aswani Kumar
>>>>>>
>>>>>> Graduate Student
>>>>>> Molecular Biophysics Unit
>>>>>> Indian Institute of Science
>>>>>> Bangalore, India.
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------------------------------
>>>>> Dr Tim Stevens Email: [log in to unmask]
>>>>> Department of Biochemistry [log in to unmask]
>>>>> University of Cambridge Phone: +44 1223 766018 (office)
>>>>> 80 Tennis Court Road +44 7816 338275 (mobile)
>>>>> Old Addenbrooke's Site +44 1223 364613 (home)
>>>>> Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
>>>>> United Kingdom http://www.ccpn.ac.uk
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------------------------------
>>>>> ------ +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)CO2-
>>>>> -------
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------------------------------
>>>>>
>>>>>
>>>> --
>>>> This message has been scanned for viruses and
>>>> dangerous content by MailScanner, and is
>>>> believed to be clean.
>>>>
>>>>
>>>
>>>
>>>
>>>
>>> --
>>> This message has been scanned for viruses and
>>> dangerous content by MailScanner, and is
>>> believed to be clean.
>>>
>>>
>>
>>
>>
>>
>> -------------------------------------------------------------------------------
>> Dr Tim Stevens Email: [log in to unmask]
>> Department of Biochemistry [log in to unmask]
>> University of Cambridge Phone: +44 1223 766018 (office)
>> 80 Tennis Court Road +44 7816 338275 (mobile)
>> Old Addenbrooke's Site +44 1223 364613 (home)
>> Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
>> United Kingdom http://www.ccpn.ac.uk
>>
>>
>> -------------------------------------------------------------------------------
>> ------ +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)CO2-
>> -------
>>
>>
>> -------------------------------------------------------------------------------
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>>
>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
-------------------------------------------------------------------------------
Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
University of Cambridge Phone: +44 1223 766018 (office)
80 Tennis Court Road +44 7816 338275 (mobile)
Old Addenbrooke's Site +44 1223 364613 (home)
Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
United Kingdom http://www.ccpn.ac.uk
-------------------------------------------------------------------------------
------ +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)CO2- -------
-------------------------------------------------------------------------------
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This message has been scanned for viruses and
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This message has been scanned for viruses and
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