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Yes, same mtz input file<br>
<br>
Sabine<br>
<br>
On 08/12/2011 03:04 PM, Antony Oliver wrote:
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cite="mid:D3F13CE3-DF1E-4E0F-AED0-BF565811BC5E@sussex.ac.uk"
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<div>Possibly a silly question - but did you use the same R-free
reflection subset in both refinements?<br>
</div>
<div><br>
Sent from my iPhone</div>
<div><br>
On 12 Aug 2011, at 13:59, "Sabine Schneider" <<a
moz-do-not-send="true" href="mailto:sabine.schneider@mytum.de">sabine.schneider@mytum.de</a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>Hello Partha,<br>
<br>
At the moment I was more looking, if it makes a difference
what comes out from Refmac, when I feed it different start
models; straight from Phaser, reset B-values, after shaking
coordinates, after shaking coordinates and SA, and so on....<br>
<br>
I assumed, if I put the output from Phenix (with R/Rfree X/X
reported by phenix) to be identical to the R/Rfree Refmac
reports as START value when it gets directly the output pdb
from phenix?
<br>
I thought the reported R/Rfree values are just something like
'model vs data'? That's what I am confused about...<br>
<br>
No twinning, no automated water building, just 1mol/asu, no
twinning<br>
<br>
Sabine<br>
<br>
<br>
<br>
On 08/12/2011 02:36 PM, Partha Chakrabarti wrote:
<blockquote
cite="mid:CABUfuXOGOAhTL81mDWUr8Gj92hsWz-HMRRJQ6oAuyJnjdWPCOQ@mail.gmail.com"
type="cite">
<div>Hi Sabine,</div>
<div> </div>
<div>I believe the comparison should be with same input, not
output of one piped into another.</div>
<div> </div>
<div>How different are the geometry? Different programs use
different algorithm and different xray:geometry term by
default. Hence, it might only make sense if the RMSD are
almost exactly the same. Furthermore, is one program
detecting NCS or twining or building waters
automatically? Then everything is blown up anyway.</div>
<div> </div>
<div>In any case, refinemt program A vs. B is an interesting
topic! I would not start one.. ;)<br>
</div>
<div>MFG,</div>
<div>Partha<br>
<br>
</div>
<div class="gmail_quote">On Fri, Aug 12, 2011 at 5:19 PM,
Sabine Schneider <span dir="ltr">
<<a moz-do-not-send="true"
href="mailto:sabine.schneider@mytum.de">sabine.schneider@mytum.de</a>></span>
wrote:<br>
<blockquote style="border-left: 1px solid rgb(204, 204,
204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
class="gmail_quote">
Hello,<br>
<br>
I am refining a structure at 2.1A solved by MR. For
curiosity I'm testing things like 'shaking' coordinates,
simulated annealing, refinement Refmac vs Phenix and so
on, to see what influence that has on stats, maps etc.<br>
<br>
For instance after MR I did a bit of shaking the
coordinates with pdbset (noise 0.1), followed by
simulated annealing in Phenix.<br>
Phenix states after SA:<br>
<br>
Start R-work = 0.2671, R-free = 0.2992<br>
Final R-work = 0.2312, R-free = 0.2666<br>
<br>
When I use the output pdb of phenix directly in Refmac
(with same mtz as input for Phenix)<br>
Refmac tells me:<br>
Initial R factor 0.2392 R free 0.2887<br>
<br>
So I am quite puzzled about the discrepancy. Or can
someone tell me if I made an error in reasoning
somewhere?<br>
<br>
Thanks a lot for the help!<br>
Sabine<br>
<br>
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