Hi Bob, Miguel,
I have been further working on the Jmol plugin for Bioclipse, which uses a CDK
model as backend, so I use the CdkJmolAdapter which we had in Jmol in the
past, but which is now in the Bioclipse plugin... and rather rewritten
because of extensive changes in the CDK with respect for reading PDB files...
Anyway, most was working up to yesterday, including the StructureIterator, for
helices/etc... Today I implemented reading of MODELs from the PDB file, which
now (as it should) results in multiple ChemModel's in CDK (if that means
anything to you...)... Therefore, I updated the CdkJmolAdapter, which works
again nicely now... ('model 1' works!)...
Anyway, my next step is to update the getStructureIterator() accordingly, but
noted that a StructureIterator() is not aware of Jmol models at all...
So, my questions: is this reasonable, i.e. are the HELIX stuff in PDB file
indeed always model independent? I know they are given in advance of the
actual "MODEL" statements, but is there nothing in the HELIX fields that
states for which model that HELIX is defined? And if there *is*, why is this
not reflected in the StructureIterator API?
BTW, I am still using Jmol 10.2 in the Jmol plugin for now. Bob, is this
behaviour different in your branch?
Egon
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blog: http://chem-bla-ics.blogspot.com/
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