On Wed, 2012-03-14 at 09:26 +0000, Dipankar Manna wrote:
> After running molrep R-factor is around 53% (100% identity), after
> rigid body refinement its showing around 49% and after restrained
> refinement its showing around 47%.
Sounds like you didn't get a solution. With 100% identity MR in most
cases works like a charm, so there must be something wrong with
1) Data processing - wrong spacegroup? Try processing your data in P1.
If MR works after that, start working up to the higher symmetry. If you
need specific advice from the bb, provide details on unit cell
parameters, space group, R-merge, chi-square etc. Best of all, post
your log files.
2) Model - without further information, it's impossible to say what the
problem is. Describe to the bb your protein - molecular weight, how
many domains, etc. Sequence identity is not the key, it's the rmsd
between your model and your structure. There are examples in the
literature when 100% identical model does not work even if broken into
domains, although it's very likely that your problems lie elsewhere.
3) Molecular replacement - sometimes the right model is rejected because
you get some conformational changes and therefore clashes. R~53% after
MR usually means that you did not find a solution. Stick in a
completely wrong model of the same size to get an idea of what to expect
when MR fails.
4) Refinement - least likely at this point, but check for the twinning.
Most of all, see if the electron density makes sense - a good test is to
remove part of the model and see if it shows up in the difference map.
Good luck,
Ed.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
