Hi Yang Li,
0) Cool down -:)
1) To see if the refinement is converged in phenix.refine is easy: just
look how R-factors change from macro-cycle to macro-cycle (this is
reported in PDB file header and in .log file). If they don't change
much, then it is "converged". If they still going down, t
Thanks for your replies. I did use default settings in phenix refine,
included TLS in it. This is an about 2.3A data, and the number Rfree used to
refine is big enough. I also kept the same Rfree in two programs. In refmac
I also tried diffenrent weighting sets--from defaut 0.3 to 0.02, TLS
inc
One point which I don't understand is how can someone compare the two
different programs when they don't use the same numbers for
xray:geometry terms? Taking the default settings for a given
resolution might not be enough.. !
On Tue, Mar 4, 2008 at 7:58 PM, Savvas Savvides
<[EMAIL PROTECTED]> w
Hi Yang
how many reflections do you have in your test-set for calculating
R-free? Too few reflections, typically less than 500, may not
constitute a statistically robust cross-validation data set, and thus may
lead to fluctuations in R-free plus a tendency for R-free to increase
as a function of
Dear Yang,
it would be better if you could provide more details about your
refinement strategies.
As I can see from your results you might have used the default values in
phenix giving you finally very low rmsd values. Refmac by default is not
using so tight restraints and even if you used tig
I'd take the one with the lowest Rfree, but it would be worthwhile to
figure out why the refinement appears unstable. phenix should work at
least as well as refmac, and as far as I am aware, use the same bond
parameters.
yang li wrote:
> Yes, I got the mtz file which can be oopened by coot
Yes, I got the mtz file which can be oopened by coot, so can I take the
phenix result?
I am customed to use refmac before, but now is confused when several choices
come out.
On 3/4/08, William Scott <[EMAIL PROTECTED]> wrote:
>
> phenix.refine also produces an mtz file by default, and that c
phenix.refine also produces an mtz file by default, and that can be
auto-opened with coot, along with the coordinates.
On Mar 4, 2008, at 7:27 AM, yang li wrote:
Since the map from phenix couldnot be opened by coot directly--or I
donnot know how to--I used refmac to get a mtz map file.
Dear All,
I have post a similar question about CNS and refmac before, now in
another structure I met a similar problem. I have an almost finished
structure, the Rfree of which
is about 0.28 by refmac. Then I used phenix to refine it, below is the
result:
REMARK REFINEMENT
