Re: [modeller_usage] structure not read in

[Modeller Caretaker <>]

Nicolas Fusseder wrote:
> I have an application which models protein sequences based on template
> structures which are found by blasting the query sequence against all
> sequences from pdbaa. The entire modeling process works fine, only when
> one of the templates structures found via blast was solved with Cryo-EM
> the modelling process fails with the following error (sorry for the nasty
> formatting):
...
> > P1;1D3E1
> structureE:1D3E:1    :1:285  :1:MOL_ID  1;  MOLECULE  INTERCELLULAR
> ADHESION MOLECULE-1;  CHAIN  I;  FRAGMENT:MOL_ID  1;  FRAGMENT  1 - 185; 
> ORGANISM_SCIENTIFIC  HOMO SAPIENS;  ORGANISM_CO:28.00:-1.00
> APVAAYVDEVLNEVLVVPNINQSHPTTSNAAPVLDAAETGHTNKIQPEDTIETRYVQSSQTLDEMSVESFLGRSG
> CIHESVLDIVDNYNDQSFTKWNINLQEMAQIRRKFEMFTYARFDSEITMVPSVAAKDGHIGHIVMQYMYVPPGAP
> IPTTRDDYAWQSGTNASVFWQHGQPFPRFSLPFLSIASAYYMFYDGYDGDTYKSRYGTVVTNDMGTLCSRIVTSE
> QLHKVKVVTRIYHKAKHTKAWCPRPPRAVQYSHTHTTNYKLSSEVHNDVAIRPRTNLTTV*

Modeller 8 only recognizes the following alignment types as denoting 
structures:
structure structureX structureN structureM
Anything else (e.g. structureE) is considered a raw sequence, and no PDB 
is read in. This has already been corrected for the next Modeller 
release; as a workaround until then, you can just edit your alignment 
file to replace structureE with structureX or similar.

	Ben Webb, Modeller Caretaker
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