CONECT records could have anywhere between 2-4 atom serial numbers and there could be entries in a CONECT record line past column 60, some programs may write shorter lines. I believe BioJava has issues parsing CONECT and LINK records of short line length, and this is still not yet fixed in 4.2.8. I might be able to submit a patch for 4.2.8 for some of these short line issues. However, I think past 4.2.x, there was a decision made to deprecate parsing of CONECT records of PDB(s) to provide Bond records. Is this correct? If possible, it would still be helpful in some cases to parse and use CONECT records to allow custom definitions of Bonds in ligands, etc.

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On Tue, Sep 5, 2017 at 10:49 AM, Spencer Bliven ***@***.***> wrote: BioJava 4.2.8 can't read the CONNECT records of PyMOL PDB files. I'm sure this was fixed in 5.0 but it would be nice to cherry-pick it into the bugfix branch. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#705>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHHQJj8rL2is10r66KbSBPo3hhUuO9MEks5sfW2EgaJpZM4PNJvf> .

-- Matt Larson, PhD Madison, WI 53705 U.S.A.

Cherry-pick PDB parser fixes to 4.2 #705

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