Thanks for all the good suggestions. This gives me a lot more things to
try.
Ursula
On Sat, Dec 13, 2014 at 2:44 AM, Claudia Millán Nebot cmn...@ibmb.csic.es
wrote:
Dear Ursula,
If you have a resolution around 2.0 A you can try some of the following:
- Expand the partial solution with
Dear Ursula,
If you have a resolution around 2.0 A you can try some of the following:
- Expand the partial solution with shelxe autotracing feature.
- Do a search with ARCIMBOLDO_LITE using the partial solution. You can fin
the program at http://chango.ibmb.csic.es/arcimboldo_lite. Then,
Dear Ursula
AMPLE is also worth trying, especially but not exclusively for smaller
and predominantly helical targets. It was originally conceived for
novel folds but you may well find ab initio modelling methods get closer
to the real structure of distant homologs than the nearest available
Hi Ursula,
I also tried to just superimpose the complete model onto the partial
solution. This results in quite nice packing, but doesn't refine. Is there
a rigid program refinement program with very large convergence?
depending on what you call very large, this may be helpful:
Automatic
Dear Ursula,
18% identity is really in the twilight zone for molecular replacement, where it
may work but there are certainly no guarantees.
However, there’s a feature in Phaser that is useful for this kind of problem,
i.e. the “rotate around” option, where you take advantage of knowing the
What is the resolution of your data? I have been able to get a solution for
my protein with 30% identity but my resolution of data was 1.4 Angs. I
believe to get a solution at 18% identity your search model has to be very
close, like using Robetta to make the 3 mer and 9mer peptides and then work
