I realized that the latest vall database that comes with Rosetta 3.2 is version 2006-05-05. Unfortunately, there is no corresponding constraint coordinate file (“vall_cst_coord.dat.”) for that database. Both database files are only available for the 2001-02-02 version. Is there a way to get the constraint coordinate file also for vall 2006-05-05?
The 2001 version contains only one-third of entries in comparison to the 2006 version.
I want to use this for fragment picking using also my experimental NMR data (can’t rely on Robetta).
Another question that might make this whole issue obsolete relates to the new fragment picker, which was used by Sgourakis et al. (JACS, 2011, Determination of Structures of Symmetric Protein Oligomers [..]). Is it possible to get this new fragment picker already in a pre-release or as a patch?
I’m told you got an answer straight from Nikolaos Sgourakis, but to archive it for the sake of other users:
“the new fragment picker application will be included in the new Rosetta 3.3 which is going to be released soon. We have already replied to Marcel internally.
His best bet right now is to use the mfr picker developed by Yang Shen at the NIH, and works ok for getting fragments.