Sorry for the delay in replying, but I can confirm your fix is working. Thanks again for all your help.
-da On Mon, Aug 15, 2011 at 07:15, Andreas Prlic <[email protected]> wrote: > Ok, got it. This happened, since you are using a Calpha-only > representation of the molecule. If you update the DisplayAFPChain > class, this should be fixed now. Since you are not using all atoms for > the alignment, ligands won't get superimposed This is something that > some users find useful... > > Andreas > > > On Mon, Aug 15, 2011 at 1:02 AM, Daniel Asarnow <[email protected]> > wrote: > > I create the AtomCache as follows: > > AtomCache cache = new AtomCache(pdbPath, divided); > > FileParsingParameters params = new FileParsingParameters(); > > params.setAlignSeqRes(false); > > params.setParseSecStruc(false); > > params.setLoadChemCompInfo(false); > > params.setParseCAOnly(true); > > cache.setFileParsingParams(params); > > My algorithmName is simply from CeMain.algorithmName or > > FatCatFlexible.algorithmName, and I use the default CeParameters or > > FatCatParameters. > > I get the StructureException I described, and then a NullPointerException > > when trying to access the artificial structure (I also test specifically > > that the artificial structure is null). > > My apologies for not adding that (about the NPE) previously, I made a > bare > > bones version of my method to remove my application-specific code and > > looking at the output made me realize I hadn't mentioned it. > > -da > > On Sun, Aug 14, 2011 at 22:09, Andreas Prlic <[email protected]> wrote: > >> > >> Hi Daniel, > >> > >> having problems to reproduce this... What is the algorithmName you are > >> using and any non standard parameters? Also, any parameters you are > >> setting on AtomCache? > >> > >> Andreas > >> > >> > >> On Sun, Aug 14, 2011 at 12:08 PM, Daniel Asarnow <[email protected]> > >> wrote: > >> > Hello again, > >> > I'm getting a null value from DisplayAFP.createArtificialStructure > after > >> > a > >> > successful alignment. It appears that the Groups in hetatms aren't > set > >> > or > >> > are missing their Atom; There is a StructureException ("no atom found > at > >> > position 0") thrown from the Group.getAtom call at DisplayAFP line 487 > >> > (inside the getAtomArray call at line 679). > >> > > >> > Here is my code: > >> > > >> > Structure structure1 = cache.getStructure("2hhb.A"); // Hb A chain > >> > Structure structure2 = cache.getStructure("2v1k.A"); // Mb > >> > Atom[] ca1 = StructureTools.getAtomCAArray(structure1); > >> > Atom[] ca2 = StructureTools.getAtomCAArray(structure2); > >> > StructureAlignment alignment = > >> > StructureAlignmentFactory.getAlgorithm(algorithmName); > >> > AFPChain afpChain = alignment.align(ca1, ca2, params); // successful > w/ > >> > correct alignment score > >> > artificial = DisplayAFP.createArtificalStructure(afpChain, ca1, ca2); > // > >> > returns null > >> > > >> > This is with the 3.0.2 snapshot JARs. > >> > I'm a missing something or is this a bug? > >> > > >> > Thanks! > >> > > >> > -da > >> > _______________________________________________ > >> > Biojava-l mailing list - [email protected] > >> > http://lists.open-bio.org/mailman/listinfo/biojava-l > >> > > > > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
