[Biojava-l] biojava Chain

[Andreas Prlic]

Hi Jian,

please don't send support emails to me directly but to the list. Chances
are that somebody else can respond faster than me, or that other users are
struggling with the same problem...

To answer your question, are you running with the "alignSeqRes" parameter
set to true?

The code below should do the job...

Andreas

AtomCache cache = new AtomCache();

 cache.getFileParsingParams().setAlignSeqRes(true);

 Structure struc = cache.getStructure("1fnt");

 System.out.println(struc);


On Tue, Jul 17, 2012 at 4:05 PM, Jian Wang <bugouzhi at gmail.com> wrote:

> Hi Andrea:
> I have a quick question regarding the Chain object in biojava3, since
> it listed you as the author in javadoc :-)...
> After loading a structure from a pdb file... I can assess the residue
> using getAtomGroup() and related methods but if i try to use the
> getSeqResGroup() and methods related to the SEQRES, everything
> is empty... the particular pdb file i loaded is 1FNT. The reason i need the
> SEQRES is because i try to assess certain atoms according to its index
> in the original sequence and the getAtomGroup() method will sometime fail
> when
> missing data are in the pdb file... any idea? thanks a lot
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> cheers
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> Jian
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