Dear Rohit
Additionally to the very good suggestions, I'd feed the structure into
the PDB_REDO server. Its a fast and easy way to detect if the refinement
strategy is correct. The server gives you a good feeling how tight the
x-ray weights need to be.
If however PDB_REDO does not manage to decrease the Rfactor gap of 7%, I
would suggest to switch to Phenix and give it a try.
If this does bring the factors down and relax the structure, let
pointless have a look into the XDS_ASCII file. Pointless and Xtriage are
two fast programs to detect if you are correct with the choice of the
space group. They give you also a first hint about twinning and the
amount of twinning.
good luck,
matthias
>>> Prem Prakash <prem...@gmail.com> 14.12.16 19.20 Uhr >>>
Dear Rohit, I am totally agree with Mark, that just R free and R work
does not decide the structure solved, you have to see other parameters
as Mark already suggested. What is and redundancy and also what is the
mosaicity? please look at these parameters too.
Best
Prem
On Wed, Dec 14, 2016 at 10:07 PM, Ashok Nayak <ashokgocrac...@gmail.com>
wrote:
Dear Rohit,
Look at what percentage of the reflections are in the Rfree set, if its
less say 5 %; and you have a good redundancy you can use 10 %. You might
like to use the other Rfree set[1 if you have already used the 0 set] or
consider using the whole set of reflections as a free set if need be if
you suspect a bias in your Rfree set.
As suggested earlier I would also look at how the Fobs and Fcalc
correlate as a function of resolution from the sigma A plot or CC*
values.
Sometimes overestimating the resolution would add up more noise and it
would give you bad R values.
and If the molecule is elongated you might have diffraction anisotropy
and in that case The R values don't come down.
I would also like to use Refmac along with Phenix; that helped in my
case.
So you would like to take them one by one and figure out carefully.
Best Wishes
Ashok Nayak
Post-Doctoral Fellow,
Department of Physiology and Biophysics
VCU Medical Centre,1101 E Marshall ST,
Richmond,VA
USA
On Wed, Dec 14, 2016 at 11:12 AM, Morais, Marc C. <mcmor...@utmb.edu>
wrote:
In addition to what others have mentioned, you might want to consider
the unpleasant possibility that part of your structure is simply built
incorrectly. Sometimes rebuilding a short loop or even a few residues
in that loop can do the trick. Look carefully for regions of your map
with poor density and/or regions of your model with poor geometry, and
see if there might be an alternate way to build that region. There is
often a psychological barrier to attempting these rebuilds, because
they are difficult (if they weren't we would have built correctly the
first time). However, once begun, it is often less painful than
expected. SA/composite omit maps can help.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
Eleanor Dodson [eleanor.dod...@york.ac.uk]
Sent: Wednesday, December 14, 2016 9:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] R/Rfree values
es - look carefully at your data quality indicators - batch scales,
Wilson plot - moments etc.. tHese can show up if there is a problem with
ice rings or crystal decay or whatever.
Then I always look at the REFMAC plot of <Fobs> v <Fcalc>
If they overlap well - good - but problems with scaling will show up
there.
Eleanor
On 14 December 2016 at 15:21, Mark J van Raaij
<mjvanra...@cnb.csic.es> wrote:
Dear Rohit,
I wouldn’t judge a structure just by the Rwork and Rfree values, but
also by the validation and other statistics (bond lengths, angles,
Ramachandran plot, map quality, fit to map, average B values). If these
are all ok, you should be able to “get away with” an Rfree of 33%.
In your email you state that you have already made a significant effort
in different refinement strategies, so perhaps there is no improvement
to be made there.
The reason for good, and reprocessing might help. Although the most likely
outcome is
that you can’t significantly improve it, but at least trying will put
your mind more at ease.
In the end, the only way to improve the structure, and R-factors, may
be to grow a better crystal, cryo-protect better and/or collect better
data - this particular crystal may just have some kind of disorder.
Greetings,
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij
> On 14 Dec 2016, at 16:02, rohit kumar <rohit...@gmail.com> wrote:
>
> Dear All,
>
> I am solving a data of 2.5 A (C121 space group). Right now the
R/Rfree values are 26/33, after many cycles of refinements (With or With
out water) the R/Rfree values still same. Zanuda suggests that the space
group seems to be correct and the model is looking fine in coot.
> Some one suggest what is the main problem.
> Should I again process my data? And what is the best way to fine
right space group (If problem with space group).
> Please tell me if you need any information regarding may data.
>
> --
> WITH REGARDS
> Rohit Kumar Singh
> Lab. no. 430,
> P.I. Dr. S. Gourinath,
> School of Life Sciences,
> Jawaharlal Nehru University
> New Delhi -110067
--
