Small bug in find_pair

[Liron Bar]

Hi everyone,

I am quite sure that I found the following bug in find_pair.

When running find_pair on 1VSP.pdb ( http://http://www.rcsb.org/pdb/explore/explore.do?structureId=1VSP ), the base pairs are associate to chain “W” instead of “w”. This capitalization is damaging since 1VSP.pdb also have chain “W” which doesn’t contains base pairs.

Did anyone else encounter this ? have anyone created a workaround ?

Thanks.

[xiangjun]

As always, I welcome bug reports related to 3DNA: the more, the merrier.

The "bug" in find_pair regarding 'w' vs 'W' chain ID issue in 1VSP is well expected, though this is the first case reported. In 3DNA, all the atom names, residue names, and chain ID characters are converted to upper case, so 'w' and 'W' is treated as the same. Thus, running find_pair against this entry gives expected result.

Making 3DNA case-sensitive with regard to chain ID is not a big deal. However, do you know of any PDB documentation showing that upper/lower case makes a difference for chain ID? How about residue name, or even the 4-letter PDB id? Did you also analyze this entry with other programs, e.g., Curves, FreeHelix? How do they deal with the chain ID issue? More generally, in all the PDB/NDB entries, how many of them have chain IDs that differ only in upper/lower cases as 'w' vs 'W' for 1VSP? In my understanding, this issue may well be due to the one letter chain ID limit in PDB format itself.

HTH,

Xiang-Jun