Dear Vikram
AMPLE tries to create ensembles by clustering the ab initio models from,
in this case, Rosetta. It has failed here because it has not found any
pair of models that are similar enough by its criteria to superpose into
a cluster. This is a sign that your 500 models are very diverse and, in
turn, that the modelling has not produced reliable results: large
clusters of similar models are the basic indication that ab initio
modelling may have produced something promising.
The explanation for the poor results lies in the size of your target.
377 residues is far above the threshold below which ab initio modelling
is expected to work well. It is currently considered to be worth trying
up to around 150-200 residues for globular proteins, somewhat larger for
membrane proteins. That limit is raised by the use of extra information
from predicted contacts
(http://journals.iucr.org/m/issues/2016/04/00/lz5010/) but 377 residues
is much larger than we have had success with using ab initio models.
It looks to me as if you may have distant homologues available. Making
an ensemble of these and seeking a well-conserved core to use as a
search model ensemble can be a productive approach, solving structures
that would not fall out easily with any single distant homologue. AMPLE
can also apply a cluster and truncate logic to distant homologues in
such cases - see
https://amplemr.wordpress.com/programs/ample/ample-tutorials/ample-tutorial-3
- automatically producing a range of differently sized shared core
ensembles and trialling them.
Feel free to contact us offline or through ccp4bb if you need more help.
Regards
Daniel
On 04/11/16 05:28, Vikram Dalal wrote:
Hi everyone,
I have run the ample for a 377 amino acids protein and generated 500
models. But I did not get any ensemble model and got error message
that could not load any ensembles after running create_ensembles. I am
here attaching the ample.log and debug.log file.
Any one suggest me why this happened?
Thanks and regards
*
*
--
Dr Daniel John Rigden Tel:(+44) 151 795 4467
Institute of Integrative Biology FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool http://pcwww.liverpool.ac.uk/~drigden/
Crown St.,
Liverpool L69 7ZB, U.K.
