Hi everyone
I am just starting with ccpnmr that I downloaded to my Linux Fedora 10. In
order to use the new iCING interface, I wanted to create a ccpnmr project
from my Aria calculation.
I encountered the following problem with the distance constraints:
For the valine and leucine residues, the methyl groups are not
stereospecifically assigned and are designated as HG1* / HG2* for valine,
HD1*/HD2* for leucine residues. Importing my chemical shifts from a nmrview
ppm.out file works fine
Set [' .20.HG11', ' .20.HG21'] as deep prochiral, non-stereo, two
resonances.
Resonance 'HGb*' ([' .20.HG21']) -- RS -- 'HG1*' -- 'HG11,HG12,HG13' atom(s)
Resonance 'HGa*' ([' .20.HG11']) / \ 'HG2*' -- 'HG21,HG22,HG23' atom(s)
but whenever I import my distance constraints, I get the following message
in the text window:
(Warning: special case - autoconnecting resonances [[' .20.HG1*'], ['
.20.HG2*']] to [' .20.HG*'].)
Set [' .20.HG*', ' .20.HG1*', ' .20.HG2*'] as deep non-stereo prochiral
(with multi group)
Added <memops.Implementation.AppDataString {application='cns',
keyword='assign', value=' .20.HG*'}> to attribute applicationData.
Copying pairwiseConstraintItems...
Resetting existing resonances...
Warning: special case - autoconnecting resonances [[' .20.HG1*'], ['
.20.HG2*']] to [' .20.HG*'].
Added <memops.Implementation.AppDataString {application='cns',
keyword='assign', value=' .20.HG1*'}> to attribute applicationData.
Added <memops.Implementation.AppDataString {application='cns',
keyword='mappingSingleMatch', value='HG2*'}> to attribute applicationData.
Copying pairwiseConstraintItems...
Added <memops.Implementation.AppDataString {application='cns',
keyword='assign', value=' .20.HG2*'}> to attribute applicationData.
Added <memops.Implementation.AppDataString {application='cns',
keyword='mappingSingleMatch', value='HG1*'}> to attribute applicationData.
Copying pairwiseConstraintItems...
Resonance 'HGa*' ([' .20.HG*', ' .20.HG1*']) -- RS -- 'HG1*' --
'HG11,HG12,HG13' atom(s)
Resonance 'HGb*' ([' .20.HG2*', ' .20.HG*']) / \ 'HG2*' --
'HG21,HG22,HG23' atom(s)
When I verify my constraint file by exporting in a different format from the
Format Converter, the distances are correctly annotated with HG1* and HG2*
but, whenever I import the whole project into iCING, iCING interpretes them
as HG**. I already contacted J. Doreleijers, supposing that there was a
problem within iCING when reading ambiguous constraints. According to him,
this is not the case and he believes it might be due to the conversion from
Aria to CCPN. You can have an insight into this issue here
:http://code.google.com/p/cing/issues/detail?id=156
Any idea ?
Thank you for your help
Beate
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