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CCPNMR  August 2011

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Subject:

Re: Antw: Re: Distance Calculation Issue

From:

Wayne Boucher <[log in to unmask]>

Reply-To:

CcpNmr software mailing list <[log in to unmask]>

Date:

Fri, 5 Aug 2011 16:13:51 +0100

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (95 lines)

Hello,

Tim says:

I don't know what the following sentence means:

'I think this should be "NOE sum", say average distance, right?'

Anyhow, the NOE contributions assignments table will show the same 
distance for two Leu methyls if they are not stereo-specifically assigned. 
We don't know which is which, structurally speaking, so cannot show a 
different distance for each resonance.

The distance in the structure viewer is the distance in the selected 
model, rather than an average, so will differ from the tables.

The table distance is an 1/r^3 ensemble average.

The bug (which was probably quite old) is fixed.

Wayne

On Fri, 5 Aug 2011, Marcel Jurk wrote:

> Hello,
>
> Thank you for your fast reply. Indeed, I forgot the screenshot.
>
> I installed the latest updates and now it looks a bit better; at least I get more realistic values.
>
> Though something is still a bit weird. In the "Assigment: NOE contributions" window under "Peak Assignments" I get a distance of 6.0 A between all 6 protons of L20 and the 3 of I9. I think this should be "NOE sum", say average distance, right?
>
> If I switch to "min dist" in the structure viewer I receive an error message (see below) and the distance depicted changes from 6.6 to 8.4 A. Confusingly, 6.6 is already different from the 6.0 A. But I assume the 6.0 is just between the 3 protons of L20.HD2* and I9. The distance in the structure viewer is for all 6 protons.
>
> Exception in Tkinter callback
> Traceback (most recent call last):
>  File "/opt/ccpnmr/python2.6/lib/python2.6/lib-tk/Tkinter.py", line 1410, in __call__
>    return self.func(*args)
>  File "/opt/ccpnmr/ccpnmr2.1/python/memops/gui/PulldownList.py", line 452, in
>    command = lambda n=index: self.setIndex(n, True)
>  File "/opt/ccpnmr/ccpnmr2.1/python/memops/gui/PulldownList.py", line 186, in setIndex
>    self.callback(obj)
>  File "/opt/ccpnmr/ccpnmr2.1/python/ccpnmr/analysis/popups/ViewStructure.py", line 712, in setDistMethod
>    self.connections[1][3] = color
> IndexError: list index out of range
>
>
> Best,
> Marcel
>
>
> Marcel Jurk
> Leibniz-Institut fuer Molekulare Pharmakologie (FMP)
> Solution NMR (AG Schmieder)
> Robert-Roessle-Str. 10
> 13125 Berlin
> Germany
>
> eMail: [log in to unmask]
> Phone: +49-30-94793223
> Fax: +49-30-94793169
>>>> Wayne Boucher  05.08.11 13.38 Uhr >>>
> Hello,
>
> There seemed to be no attached example, but the first thing I would
> suggest is to make sure that you have the latest updates.
>
> Tim also says:
>
> I assume that the distance is that reported in a table? And if so which
> table specifically?
>
> Is this the "NOE sum" distance? (Which isn't a real distance but rather
> the apparent one used for violation analysis). Two methyls with identical
> shifts will mean that there are 6 protons all contributing to the peak
> intensity...
>
> Does using the "minimum" value method for distances help?
>
> Wayne
>
> On Fri, 5 Aug 2011, Marcel Jurk wrote:
>
>> Dear all,
>>
>> I noticed that analysis seems to miscalculate distances between degenerate methyl-protons. The attached example is only one of a few I came about. In this case the actual distance is calculated to be 5.96 A, which can't be true. Using pymol and measuring only heavy-atom distances I think the true distance is somewhere around 10-11 A.
>>
>> What could be the reason for this?
>>
>> I am still using 2.1.5, since a repeated attempt to update did not work.
>>
>> Best regards,
>> Marcel
>>
>

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