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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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</div>
<br>
</blockquote>
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