Dear All,
Thank you for your suggestions. Many of you asked what the occupancies
were in the region and they were all one, so partial occupancy was not
the problem.
I was using TLS restraints during the refinement when this problem
happened. Given the suggestions that TLS may be a problem and that might
be causing the low B-factors, I went back and re-ran the refinement
without TLS and the problem disappeared. Then I submitted my latest file
to the TLSMD server for new restraints and the next round of refinement
got rid of the problem. The B-factors increased to normal levels (~15
compared to ~5 before) so it seems to have done the trick.
Thank you to everybody for their help,
Judith Reeks
ja...@st-andrews.ac.uk
School of Chemistry
University of St Andrews
On 01/03/2011 17:28, Mark Robien wrote:
Hmm - kinda interesting
In addition to the sorts of things suggested by Mark van Raaij, older
versions of Refmac
were prone to have a phenomenon with B factors - once they get over a
certain level, the algorithm
has a very hard time bring them back down, even when the data suggests
it.
I've usually seen it with much higher B factors than you seem to have
here - for example, loops where the B's
are actually 40-60, but previous rounds of refinement have the B
factors 60-80 or higher.
Judging from the coot screen & the residues you are focusing on, I
doubt that is the answer (unless you also
have a TLS model, in which case I'd wonder). If you do have TLS -
well, things get more complicated; for example,
is this the edge of a TLS domain?
Nonetheless, you could try the solution for the problem that I
describe - which is to reset all the B factors to a (very)
low B factor - maybe even as low as 2.0 (lower?), and then another
round of refmac - with a sufficient number of
cycles - will re-refine the B (and xyz), thus escaping the region of
refinement space that has a very weak gradient.
A variant approach that might be appropriate - similarly reset the B
for the (?small) region of your model that has the problem.
Sadly, it's been awhile since I did any refinement myself - but the
uppsala suite had some of the nicer tools for resetting B within pdb
files, without having to do it manually (ugh - not appealing) - or
writing an adhoc awk script (a very easy alternative, if you're
familiar enough).
Mark Robien
On 3/1/2011 10:32 AM, Judith Reeks wrote:
Dear All,
I am currently refining a structure using the latest experimental
version of Refmac (5.6) and there seems to be a problem with my Fo-Fc
map. There is a region where I have fitted residues to the electron
density but after refinement there is still positive electron density
assigned to the region despite the fact that residues fit the
electron density (see link below for a screenshot). Multiple rounds
of refinement have yet to get rid of this problem. I have checked the
PDB file and there does not appear to be any problems with this
region. Has anybody seen something like this before?
http://i1083.photobucket.com/albums/j382/jreeks/Screenshot2011-03-01at1613402.png
Regards,
Judith Reeks
ja...@st-andrews.ac.uk
School of Chemistry
University of St Andrews
