[Xplor-nih] Xplor-nih Digest, Vol 52, Issue 12

[John Kuszewski]

On Jun 18, 2007, at 5:12 AM, Gary S. Thompson wrote:

>>> #note use of list command to protect string from commands such as
>>> $noe peaks
>>> eval match3d \
>>>   -peakList [list [$noe peaks]] \
>>>
>>>
>>>
>>
>> This isn't necessary.  [$noe peaks] returns a TCL list structure.
>> Wrapping it in another list will almost certainly break something.
>> Same thing with wrapping the readSpectralRange calls--those procs
>> also return TCL lists.
>> If you're getting errors, there's probably something else wrong.
>>
>>
>>
> Ah but I am afraid I think it is ! its because I do the eval to get  
> the
> folding flags in.

Ack--you're right.  My eye skipped right over the eval call for some  
reason.


>>
>> You do, depending on how your spectra were processed, and depending
>> on exactly what Frank's headers are giving you.
>> The values in the spectral range flags need to be the *exact* shifts
>> about which the folding/aliasing takes place.   Remember that
>> in the end, we're going to try to match peak positions to folded
>> shift values to within a rather tight tolerance (0.02 ppm in 1H, 0.2
>> ppm in heavyatoms),
>> so even small errors in the spectral range will screw things up.
>>
>>
>>
> indeed this wthat I guessed! As it turns out in our current setup we
> have no folded peak lists (we unfolded the lists in analysis)

In that case, you can just give spectral ranges for each dimension  
that are larger
than the spread of the unfolded peak locations, and indicate what  
sign your
unfolded peaks have.  The matching should go just fine.

>> All of which, I notice, are related to stuff that's in the manuscript
>> I'm working on now.  :-)
>>
> I look forward to that then!

Heh.  So do Marius and Charles.

--JK