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Hi George,
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display: inline !important; float: none;">phenix.model_vs_data </span><a class="moz-txt-link-freetext" href="http://www.phenix-online.org/documentation/reference/model_vs_data.html">http://www.phenix-online.org/documentation/reference/model_vs_data.html</a>
is giving you statistics in resolution bins. The gui name is
comprehensive validation.<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 01/13/2015 05:24 PM, George
Devaniranjan wrote:<br>
</div>
<blockquote
cite="mid:CAFU65Pd-9P4n8d6jpT3Oy6Nk1P5sYdEaMWv-tjxBpdQe_9JuAA@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Pavel,
<div>Thank you.
<div><br>
</div>
<div>If I wanted to compare a RCSB structure's highest
resolution shell R with my refined highest resolution shell
R.</div>
<div><br>
</div>
<div>Do I generate a log file with the binned R <u><b>for the
RCSB structure</b></u> by running phenix.refine but with
<b><u>strategy='none' </u></b></div>
<div><br>
</div>
<div>or is there a way to generate these binned R factors for
the deposited structure without running a refine cycle with
none as strategy?</div>
<div><br>
</div>
<div>Thank you,</div>
<div>George</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Jan 13, 2015 at 11:04 AM, Pavel
Afonine <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi George,<br>
<br>
look in phenix.refine log file: it prints statistics in
resolution bins (R-factors, completeness, number of
reflections, <F>, etc); so you can take the number
from highest resolution shell. Of course the definition of
"highest resolution shell" is somewhat arbitrary, and also
depends on how you do binning. <br>
<span class="HOEnZb"><font color="#888888"> <br>
Pavel</font></span>
<div>
<div class="h5"><br>
<br>
<div>On 1/13/15 6:48 AM, George Devaniranjan wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>I am sorry to ask another question, this is
related to the above hence following up on this
thread.</div>
<div><br>
</div>
<div>I can calculate R/R-free using the validation
tool but how does one calculate the </div>
<div><br>
</div>
<div>R factors for the highest resolution shell ? </div>
<div><br>
</div>
<div>Thank you,</div>
<div>George</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Jan 13, 2015 at
2:31 AM, Tim Gruene <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:tg@shelx.uni-ac.gwdg.de"
target="_blank">tg@shelx.uni-ac.gwdg.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">Hi Pavel,<br>
<br>
I was puzzled and misled by the choice of
terms and implied an intent<br>
that apparently wasn't there.<br>
<br>
Best,<br>
Tim<br>
<div>
<div><br>
On 01/12/2015 10:01 PM, Pavel Afonine
wrote:<br>
> Hi Tim,<br>
><br>
> it is a shame that I can't remember
that particular paper where I think<br>
> Randy Read or Axel Brunger have
demonstrated that phase error and Rfree<br>
> are well correlated. So if you get
best Rwork and Rfree chances are you<br>
> also get best map too.<br>
><br>
> All the best,<br>
> Pavel<br>
><br>
> On 1/12/15 3:54 AM, Tim Gruene wrote:<br>
>> Dear George,<br>
>><br>
>> what are the reasons why are you
trying to reduce the R/Rfree instead of<br>
>> producing the best possible map?<br>
>><br>
>> Best,<br>
>> Tim<br>
>><br>
>> On 01/11/2015 11:24 PM, George D
wrote:<br>
>>> Hi Phenix users,<br>
>>><br>
>>> I was looking at the
phenix-refine manual and it mentions
running<br>
>>><br>
>>> optimize_mask=true<br>
>>><br>
>>> optimize_xyz_weight=true<br>
>>><br>
>>> optimize_adp_weight=true<br>
>>><br>
>>><br>
>>> I was wondering what else I
could try to bring the Rw/Rf down by 1-2%<br>
>>> if possible, just wondering
if there are any other strategies I could<br>
>>> try.<br>
>>><br>
>>><br>
>>> Thank you,<br>
>>><br>
>>> George<br>
>>><br>
>>><br>
>>><br>
>>>
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>><br>
>>
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<br>
</div>
</div>
<div>
<div>--<br>
Dr Tim Gruene<br>
Institut fuer anorganische Chemie<br>
Tammannstr. 4<br>
D-37077 Goettingen<br>
<br>
GPG Key ID = A46BEE1A<br>
<br>
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