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
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Aleksandar Bijelic, MSc.
Institut für Biophysikalische Chemie
Universität Wien
Althanstrasse 14
A-1090 Wien
Tel: +43 1 4277 52536
e-Mail: [email protected]
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