[modeller_usage] wrong asparagine and glutamine side chains

[David Rodríguez <>]

>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.

In order to overcome this, I used the "mutate_model.py" script, to try the trick of mutating glutamine for itself, but didn't work. I wonder if anyone know a way to detect and/or correct those residues with a Modeller script (I know other programs that can do it, but using an exclusively Modeller pipeline will make things much easier).

Thanks in advance,

-- 
David Rodríguez Díaz, PhD Student

Fundación Pública Galega de Medicina Xenómica (SERGAS)
E-mail: david.rodriguez.diaz at usc dot es

Attachment: gln.pdb
Description: Protein Databank data