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How to make mini robust against malformed PDBs
Author
Steven Lewis smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om

This document was orginally written 6 Apr 2010 by Steven Lewis. This document was last updated 26 Nov 2012 by Steven Lewis.

New_Library contains code for this purpose

Rosetta's PDB reader is fragile, and the PDB is not particularly carefully curated. There are lots of PDBs that cannot be read in by Rosetta (several thousand fail to read in at all), and many more that cannot be scored for some reason. Unfortunately, these bad PDBs tend to cause Rosetta to crash rather than exit gracefully. This document describes how to "robustify" Rosetta so that it will not crash when encountering a bad PDB.

When would I use it?

You might want to robustify Rosetta if you are going to do a small-nstruct, large -l experiment. In my case, I ran with -nstruct 1 against literally the entire PDB, once in 2010 (?) and once in 2012.

Why are these not set up by default?

The changes that have to be made cause a significant performance hit to Rosetta (particularly the vectorL change). These should not be left on by default. A better question is, why does no one improve the PDB reader to more gracefully catch these errors. The answer to that is: why don't you do it, and make this page obsolete?

Okay, I'm convinced, how do I do it?

You NEED to make a few changes:

This combination of changes will cause vector overruns to throw exceptions inside runtime_assert, instead of crashing or causing segfaults. jd2 will catch the exceptions and treat the failed PDB as a failed job, print an error message, and cleanly move on to the next PDB in your list.

There are some other suggested changes:

How many PDBs are bad?

The PDB as of mid-November 2012 contained 86008 PDBs. Of these, 6460 crash in the PDB reader. Another 40 crashed from vector1 runtime_asserts, and 6 from containing only single-residue chains, somewhere in the AnchorFinder executable. (These 46 may not be universally malformed, depending on what AnchorFinder does differently from your application).