Hi Charles
Here is the output you asked for.
Using averaging type: center
Violated NOE restraints in potential term: cs ( threshold=0.5 )
id atoms in set i atoms in set j calc obs range
diff dev
----------------------------------------------------------------------------
------------
0 ( A 191 TRP HE3) ( A 194 TRP CE2) 5.658 1.5..3.5
2.158 0
( ) ( A 194 TRP CZ3)
Using averaging type: sum
Violated NOE restraints in potential term: cs ( threshold=0.5 )
id atoms in set i atoms in set j calc obs range
diff dev
----------------------------------------------------------------------------
------------
0 ( A 191 TRP HE3) ( A 194 TRP CE2) 4.981 1.5..3.5
1.481 0
( ) ( A 194 TRP CZ3)
Apparently everything works as expected. We have to dig deeper into our data
to find out why we end up with the result we do.
Thanks a lot for your help,
Kaare
On 11/2/11 7:28 PM, "Charles Schwieters" <charles at schwieters.org> wrote:
>
> Hello Kaare--
>
>>
>> We also thought that the center averaging would work. In the
>> calculations we do, however, get two distinct orientations of the
>> first Trp, one where HE3 is close to CE2 of the second Trp and one
>> where it is close to CZ3.
>>
>> From browsing the old Xplor manual the SUM averaging is apparently forced
>> when using OR in the atom selection. I guess the center averaging only works
>> when you select several atom using a wild-card. See: http://nmr.cit.nih.gov/
>> xplor-nih/xplorMan/node380.html#noe-ambiguity
>>
>
> Right there is an issue with center averaging and the ASSIGN ... OR
> syntax, hopefully your ambig.tbl doesn't have any of these.
>
>> The way we set up the noe term was the following:
>>
>> for (name,scale,aveType,file) in [('all',1,'sum',"nonredun_20110929.tbl"),
>> ('cs',1,'center',"ambig.tbl")
>> ]:
>> pot = create_NOEPot(name,file)
>> pot.setScale(scale)
>> pot.setAveType(aveType)
>> noe.append(pot)
>>
>> where the HE3 to CE2/CZ3 restraint is in the ?cs? list.
>
> Humor me and try replacing the 'center' with a 'sum' and see if there
> is any difference. Particularly in output if you add (right after noe
> setup:
>
> from simulationTools import analyze
> print analyze(noe)
> import sys; sys.exit(0)
>
> best regards--
> Charles
>
>
> --
> Charles Schwieters email: Charles at Schwieters.org
> www: http://schwieters.org/cds
> phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
>
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