Dear Kaare,
I would suggest making explicit, relatively tight (+- 0.02 angstroms) distance
restraints from your proton to every atom in the 6 member ring. You will need
to account for the van der Waals radii, and calculate what the exact distance
should be from a proton sitting in the center of the ring to each carbon atom
of the ring.
Keith
>-----Original Message-----
>From: xplor-nih-bounces at nmr.cit.nih.gov [mailto:xplor-nih-
>bounces at nmr.cit.nih.gov] On Behalf Of Kaare Teilum
>Sent: Wednesday, November 02, 2011 8:58 AM
>To: xplor-nih at nmr.cit.nih.gov
>Subject: Re: [Xplor-nih] Pseudoatom in aromatic ring
>
>Hi Eiso
>
>Thanks for the quick reply. I made a typo in the post. We did set
>AVERAGE=CENTRE but apparently xplor forces SUM when you use OR in the
>ASSIGN
>statement. So the question is how to get around this.
>
>Kaare
>
>On 11/2/11 1:53 PM, "Eiso AB" <eab at zobio.com> wrote:
>
>> Kaare Teilum wrote:
>>> Dear Charles / all
>>>
>>> I have a question concerning an atom selection in a special case. I
>need to
>>> make
>>> a restraint between a proton and the exact center of an aromatic ring
>(in
>>> this
>>> case the 6-ring in a tryptophan indole). So far, I've tried to define
>it as
>>> an
>>> NOE in the following way:
>>>
>>> ASSIGN (RESID 19 AND NAME HE3) ( (RESID 20 AND NAME CE2) or (RESID 20
>AND
>>> NAME
>>> CZ3) ) 2.5 1.0 1.0
>>>
>>> and setting avetype to SUM for this restraint. It was evident, that
>the 19
>>> HE3
>>> either was restrained to CE2 OR CZ3 and not in between them. How
>should I
>>> write
>>> the NOE in order to select the center of the tryptophan ring - is
>this
>>> possible?
>>>
>>
>> why 'SUM' and not 'CENTER' ?
>>
>> from
>> http://nmr.cit.nih.gov/xplor-nih/doc/current/xplor/node379.html#5077 :
>>
>> '''
>> For AVERage=CENTer, the distance between selected sets of atoms is set
>to the
>> difference between the geometric centers of the atoms,
>> \begin{displaymath} R= (r^{1}_{center} - r^{2}_{center})
>\end{displaymath}
>> '''
>>
>>
>> goodluck, Eiso
>>
>>
>>
>
>
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