Error running on Alphafold models

[sbliven]

Running CE-Symm on alphafold models give an error:

$ runCESymm.sh -J AF-A0A024R1R8-F1-model_v2.cif
Structure       NumRepeats      SymmGroup       Reason
594 [pool-2-thread-1] ERROR workers.CeSymmWorker - Could not complete job: AF-A0A024R1R8-F1-model_v2.cif
java.lang.IllegalArgumentException: ID can not be null
        at org.biojava.nbio.structure.PdbId.<init>(PdbId.java:78) ~[cesymm-2.2.1.jar:2.2.1]
        at org.biojava.nbio.structure.URLIdentifier.toCanonical(URLIdentifier.java:125) ~[cesymm-2.2.1.jar:2.2.1]
        at org.biojava.nbio.structure.URLIdentifier.reduce(URLIdentifier.java:130) ~[cesymm-2.2.1.jar:2.2.1]
        at org.biojava.nbio.structure.align.client.StructureName.reduce(StructureName.java:511) ~[cesymm-2.2.1.jar:2.2.1]
        at org.biojava.nbio.structure.align.util.AtomCache.getStructure(AtomCache.java:504) ~[cesymm-2.2.1.jar:2.2.1]
        at workers.CeSymmWorker.run(CeSymmWorker.java:58) [cesymm-2.2.1.jar:2.2.1]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130) [?:?]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630) [?:?]
        at java.lang.Thread.run(Thread.java:832) [?:?]

The error occurs in both PDB and CIF files

[josemduarte]

This looks like a consequence of the new PdbId class handling, introduced in biojava/biojava#950

In principle the parser should not try to set a PDB id for AlphaFold case. But it looks like it is trying that. Do you know if you are parsing PDB format or mmCIF format?

[youkha]

I have errors on pdb structures as well ... BTW Happy New Year!

…

On Tue, Jan 18, 2022 at 12:26 PM Jose Manuel Duarte < ***@***.***> wrote: This looks like a consequence of the new PdbId class handling, introduced in biojava/biojava#950 <biojava/biojava#950> In principle the parser should not try to set a PDB id for AlphaFold case. But it looks like it is trying that. Do you know if you are parsing PDB format or mmCIF format? — Reply to this email directly, view it on GitHub <#113 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD35NIJONTN64NEROMQBKKTUWWPCZANCNFSM5MHXMBTA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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[josemduarte]

@sbliven this is fixed in biojava 6.0.5

[sbliven]

Thanks @josemduarte