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On 9/1/11 6:49 PM, Pavel Afonine wrote:
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Hi Jose,<br>
<br>
DANO and SIGDANO are not used in refinement. <br>
<br>
Resetting ADPs to an average value, and performing ~5 macro-cycles
of refinement with SA and weights optimization typically should be
sufficient. Make sure you are using the latest PHENIX version from
nightly builds:<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.phenix-online.org/download/nightly_builds.cgi">http://www.phenix-online.org/download/nightly_builds.cgi</a><br>
<br>
Let me know if you have any questions.<br>
<br>
Pavel.<br>
<br>
On 9/1/11 9:25 AM, Jose Arcadio wrote:
<blockquote cite="mid:4E5FB1F7.9090309@tuebingen.mpg.de"
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Dear phenix.refine community: <br>
<br>
I am solving a protein structure using experimental phasing. In
order to do that I combined two derivative isomorphous datasets
into a double SAD experiment (to increase the individual weak
anomalous power from each dataset) using SHARP.<span style="">
</span>My resolution is 3.2 A, and the space group is C2221. <br>
<br>
I managed to build a model using the density-modified phases
from SHARP. Then I started refining against one of my derivative
datasets because my native dataset is non-isomorphous due to the
heavy meal soaking.<span style=""> Then </span>I made two
mistakes :( <br>
<br>
1. I did not realize at the beginning of my refinement-building
rounds that I was refining against the dataset that showed the
worst statistics. <br>
<br>
2. I was using a dataset with only FP and SIGFP but not DANO and
SIGDANO. <span style=""> </span>I used the phases from my SHARP
map (also the experimental phase restraints) <br>
<br>
Now I did a new run of refinement using my best dataset (better
statistics) and also including the anomalous data FP, SIGFP,
DANO and SIGDANO. Obviously, my R-work and R-free got pretty
much better.<br>
<br>
Nevertheless, the R-free was better than R-work at the beginning
of the run, at the end of the refinement R-free and R-work
inverted as usually (being R-free worst than R-work) r_work =
0.2582 r_free = 0.2888 . Certainly, there was a mistake with a
new assignment of the free set of reflections. Now I am aware
that the set of free reflections has to be the same all over the
refining procedure.<span style=""> </span> <br>
<br>
Here are the questions<br>
<br>
How can I be sure that my R-free is still a safe cross
validation of the correctness of my structure? <br>
<br>
Is it useful to perform a round of simulated annealing in order
to erase any wrong information in my model and start the
refinement rounds again?<br>
<br>
Do you have any suggestions? <br>
<br>
All the best <br>
<br>
Jose Farias
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<br>
</blockquote>
<br>
Thanks a for the help Pavel and Nat. <br>
<br>
In order to reset ADPs to an average value, shall I use:
set_b_iso=30 ? <br>
<br>
Could you suggest a good starting point for wxc_scale and wxu_scale
for my resolution (3.2 A). Or maybe I should estimate these values
empirically? <br>
<br>
I would also like to include the heavy metals in my structure, in
this case I guess it is important to have DANO and SIGDANO as you
also suggested.<br>
<br>
<br>
Best regards <br>
<br>
<br>
Jose<br>
<br>
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