Hello,
I would certainly try the "usual approaches" (map coefficients that are
less sensitive to model-bias, i.e. Sigmaa; OMIT maps - there are several
of these which can be calculated). In addition, you may have a look at
the approach of Liu and Xiong (2014, J. Mol. Biol. 426, 980-993). It is
a well known technique (applying a negative temperature factor to
amplitudes, for map sharpening) but this paper describes a systematic
study indicating improvement whatever the situation.
As usual in macromolecular crystallography, confidence is gained by the
use of several approaches.
HTH,
Fred.
On 29/04/15 13:16, Aleksandar Bijelic wrote:
Dear CCP4 users,
I am currently solving a structure (2.8-2.9 A resolution) of a protein
complexed with a ligand using MR with the apo-form of this protein as
model (resolution of the model is 2.4). After MR-phasing I performed a
regular autobuild run giving me good outputs and thus I refined the
best pdb leading to good values according to R-values and geometry,
however, the denstiy doesn´t look well (but I think it´s due to the
moderate resolution). Now I want to get sure if the side chains which
are involved in the ligand binding are correctly positioned. However,
the active site is suspicously similar to the active site of the model
(apo-form) and so I am afraid that this could be due to model bias.
My question is how to check and to get rid of the bias (if present) at
this stage (after several refinements). I read the publication of
Terwilliger about iterative-build OMIT maps but since I am a bloody
novice in this field I didn´t really understand it. I originally
thought iterative-build OMIT maps are performed to compare the output
map with one´s map in order to detect uncertainties, but what to do
next? Or should I start from the beginning but how to proceed than,
what should I do (I am using Phenix via GUI) ... Is it possible and
reasonable to run autobuild with iterative omit map option? Or is it
only reasonable if experimental phases are available? I didn´t run
iterative-build OMIT maps yet because I am not sure how to run it
correctly (what method is the best?) and at my institute the run will
take more than 1 day and I don´t want to block one computer until I am
not sure if it is reasonable. I hope you can give me some advice and
help me. Thank you in advance.
Regards,
Aleks
--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
Campus EPN
71 avenue des Martyrs
CS 10090
F-38044 Grenoble Cedex 9
Tel: +33 457428605
Fax: +33 476501890
