Hi all,
I looked again careful in the respective files and it turns out that all
B-Factors of the protein chains which are treated with TLS are refined
to the lowest possible value of 2.00 for all atoms!
A workaround is to use the option to set the initial B-factor to 20.0 in
the GUI and than the refinement finally works. I haven't yet figured out
what goes wrong in Refmac, but it seems in the B-Factor refinement step
something gets not treated quite right.
Cheers
Christian
Am 18.06.2015 um 21:58 schrieb Shane Caldwell:
Hi Christian, I've seen this behaviour as well. I'm not an expert but I
rationalized the situation as the TLS parameters for an incomplete model
getting overfit as the missing/wrong parts of the model pull on the TLS
parameters. REFMAC doesn't alternate between TLS and coordinate
refinement, so you can get stuck in a local minimum that moving atoms
and refining individual B-factors won't get you out of. As more of the
model is built correctly, the drift of this refinement gets less and less.
I've found that refining comparatively few TLS cycles (I usually do 3)
before the restrained refinement tends to avoid this problem most of the
time - don't let the TLS refinement converge. Sometimes I'll let the
coordinate step converge, then run another TLS refinement to bootstrap
things along, but usually the stats only marginally improve at that
point. In cases where I've made substantial rebuilds, it's sometimes
been necessary to turn off TLS and refine without it like you do, then
re-introduce the same TLS groups, setting the B-factors to fixed values.
Not really ideal, but it gets there. Hopefully others have some more
theoretically-sound advice.
A good thing to look at doing, especially if TLS is behaving weirdly, is
to check with the PARVATI server
(http://skuld.bmsc.washington.edu/parvati/). If your TLS group
boundaries set off flags, you have some more work to do on the refinement.
Shane Caldwell
McGill University
On Thu, Jun 18, 2015 at 4:30 PM, Christian Roth
<christian.r...@bbz.uni-leipzig.de
<mailto:christian.r...@bbz.uni-leipzig.de>> wrote:
Hi all,
I refine a structure with TLS and restrained refinement in Refmac.
After the run finished, I fixed a few outliers manually in Coot,
saved that file and used that with the original TLS file from TLSMD
for the next round of refinement. As soon as the restrained
refinement starts the R-factors are going up and stabilise than at a
higher values compared to the previous run.
If I switch of the TLS refinement and just do restrained refinement
with the same input files the R-values start initially at a higher
values and than decrease till they stabilise. Unfortunately the
final values are about 1.5 % higher, compared to the run with TLS
before manual rebuilding. So TLS seems to me beneficial and I would
like to use it, but somehow a strange combination of wrong files?,
wrong parametrization? or whatever prevent me of doing that.
Has anyone an idea what might be the cause of that strange behaviour.
Thank you very much in advance.
Cheers
Christian
--
Christian Roth
Strukturanalytik von Biopolymeren
Fakultät für Chemie und Mineralogie
Universität Leipzig
Deutscher Platz 5
04103 Leipzig
Email christian.r...@bbz.uni-leipzig.de
