Hello Modellers users:
I want to analyze a set of PDB models, all with same sequence (84 Aa peptide) but different conformations (obteined by different methods). So I used the compare.py script from tutorial to do a first classification from structure but I get the error:
_modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 0
I search this error, and most of the time is related to too different proteins that do not align well in sequence. But in my case all the protein are the same sequence!. Even I add a write step between malign() and malign3d() in the script so I see a perfect sequence alignment.
Some idea? could be the reason that some structures are too different?
Felipe Villanelo Lizana Bioquímico Laboratorio de Biología Estructural y Molecular Universidad de Chile
"La curiosidad no mató al gato, sino que la falta de ella"
On 8/21/14, 3:36 PM, Felipe Villanelo wrote: > _modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < > 3: 0 > > I search this error, and most of the time is related to too different > proteins that do not align well in sequence.
Close - it means that they do align well *structurally*. Of course, if they don't align well in sequence they're probably not going to align structurally either, but that's not always the case. Are your structures very different (structurally)?
Ben Webb, Modeller Caretaker