For reference, this seems to be working as it ought after a subsequent
fix, i.e. you can load and use substructures for distances.
One general point of caution is to load the structure into the right
molecular system, noting that the system will naturally aim for the best
matching sequence, but this may not be the one with assignments. Loading a
substructure into a brand new molecular system will give a perfectly
matching sequence, but these new atoms will not have assignments and so
won't be a source of distances for resonances assigned elsewhere (even if
the numbering is the same).
T.
> As I wrote my truncated model is now loaded, but no distances are
> calculated or at least displayed in the "NOE Contributions" "Possible
> Assignments" dialogue. Clicking any possible assignment in this dialogue
> does not produce an error message in the terminal window. This is also
> true for sequential amino acids where a distance calculation should be
> possible.
>
>> While Analysis has allowed the use of close homologues and mutant
>> structures for some time it did not match structures with large
>> missing regions to existing chains.
>>
>> Now though I have updated both v2.1.5 and v2.2.1 so that a structure
>> for only part of a chain may be loaded, however the match must be
>> perfect, i.e. all the residues of the structure must be present in the
>> chain. The user will be warned about truncations of more than ten
>> residues and has the chance to cancel. Also, the structure will only
>> be associated with a longer chain if there is not a better, shorter
>> matching one in a project. Hence if the structure was previously
>> loaded as a separate molSystem/chain then this should be deleted first.
>>
>> If the structure is loaded into the longer chain that carries
>> assignments then operating the NOE contributions system should be no
>> problem.
>>
>> Regards,
>>
>> Tim
>>
>>> I need some help with the NOE contributions option in Analyis.
>>>
>>> The issue arises because I have a 2 domain protein and did the
>>> assignment on spectra with full-length protein. Unfortunately, I have
>>> only models of the individual domains and not of the whole protein.
>>> The pdb file I would like to use is for residues 131-273 and loaded
>>> as #2 in the "Structure:Structures" option and was given the chain
>>> name "B", whereas I did my assignment on "A" (resi 2-273). The "NOE
>>> Contributions" option under the "Peak List & Display Settings" does
>>> not list structure #2, so I can't chose it as a template for
>>> assignment. Since I think this stems from the fact that the models
>>> have different chains (although the sequence is the same, if
>>> truncated), I copied the assignment from chain A to chain B via the
>>> CopyAssignments option and the "Between Molecule Chains" tab. All
>>> residues of chain B (131-273) have now the same associated resonances
>>> as their equivalents in chain A.
>>>
>>> Probably this is only about ticking a forgotten box, but I appreciate
>>> any hints.
>>> Thanks very much in advance.
>>>
>>> Best regards,
>>> Marcel
>>
>>
>>
>> -------------------------------------------------------------------------------
>>
>> Dr Tim Stevens Email: [log in to unmask]
>> Department of Biochemistry [log in to unmask]
>> University of Cambridge Phone: +44 1223 766018 (office)
>> 80 Tennis Court Road +44 7816 338275 (mobile)
>> Old Addenbrooke's Site +44 1223 364613 (home)
>> Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
>> United Kingdom http://www.ccpn.ac.uk
>>
>> -------------------------------------------------------------------------------
>>
>> ------
>> +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)CO2- -------
>>
>> -------------------------------------------------------------------------------
>>
>
> --
> 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: +49-030-94793169
>
-------------------------------------------------------------------------------
Dr Tim Stevens Email: [log in to unmask]
Department of Biochemistry [log in to unmask]
University of Cambridge Phone: +44 1223 766018 (office)
80 Tennis Court Road +44 7816 338275 (mobile)
Old Addenbrooke's Site +44 1223 364613 (home)
Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23
United Kingdom http://www.ccpn.ac.uk
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