On 6/24/10 3:42 AM, David Rodríguez wrote:
From time to time I find in generated models wrong asparagine and glutamine side chains (see attached PDB for a glutamine example), either with automodel or loopmodel classes. It is not reproducible, it happens in certain runs, and within the same one it only happens in one residue of one model. I've been looking for it to be documented, but I found nothing related.
This is either a sampling or a scoring issue. Neither sampling nor scoring are "perfect" in any sense in Modeller. Either the scoring is incorrect - i.e. Modeller genuinely thinks those wonky configurations are better than correct ones - or the sampling is insufficient - i.e. the optimizer has got stuck in a local minimum, and is unable to escape from it and find the correct conformation. I suspect it's the sampling, in which case the usual procedure of simply building more models and relying on assessment to discard the incorrect ones should be sufficient.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage