Hi Dipankar
If you've been reading the ccp4bb for more than a couple of weeks,
you should have realised that reducing your R-factor is *not* the
goal of refinement - having a low R-factor is one of the consequences
of having built your model well and of having performed a good
refinement. Don't try to reduce all the thousands of observations,
days (weeks, months, years...) of work and thousands of pounds/
dollars/Euros,rupees to a single number.
If you really don't know what you should be doing, and this is your
first time, you should do the following, all of which will give you
much more useful information than you can possibly get from ccp4bb.
(1) Find a copy of David Blow's book "Outline of Crystallography for
Biologists" and read it, especially chapter 12 (Structural
Refinement). This will take no more than a couple of days if you are
reasonably happy with what you are doing.
(2) Find a copy of Bernhard Rupp's book "Biomolecular
Crystallography" and read the chapter on "Model building and
Refinement" (also, coincidentally, chapter 12). Keep the book next to
you while you are learning protein crystallography.
(3) Actually, this should be the *first* thing you should do. Talk to
experienced crystallographers in your lab. If they are any good at
all, they will explain to you what you should be doing and why.
(4) Go on a course - Aurigene should find it well worth the
investment in paying for their employees to attend one of the various
intensive protein crystallography courses that take place around the
world. At these courses, you get the chance to meet and discuss
issues with global leaders in the field - and learn a huge amount.
(5) (Worst option) Read past posts on this on the ccp4bb - they
should only make you realise that you should have done (1) to (4)
above anyway.
HTH,
On 14 Mar 2012, at 09:26, Dipankar Manna wrote:
Dear Crystallographers,
Can anybody guide me how to reduce R-factor, means which are the
basic parameters I have to look for to reduce the R-factor during
refinement. I am newly learning the refinement. After running
molrep R-factor is around 53% (100% identity), after rigid body
refinement its showing around 49% and after restrained refinement
its showing around 47%. Highest resolution is 2.5A.
Regards
Dipankar
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