<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>The application we're talking about here is using a model that hasn't seen all the data in refinement to decide how far there's real signal in the data that were measured. We used that for the structure of 1bos (carbohydrate complex with Shiga-like toxin B-subunit), where the data should have been cut off at about 3.5A according to normal I/sigma criteria. However, by including weak data to 2.8A (helped in no small measure by 20-fold NCS), we were able to get very clear density for the bound carbohydrate. We validated the use of the weak data by taking the molecular replacement model before refinement and computing a SigmaA curve against all the data. The SigmaA values were significantly above zero up to 2.8A (indicating a correlation with the observed data, and since we hadn't done any refinement against those data this confirms that there's really some useful signal there), but dropping off dramatically at higher resolution. Axel has done similar things with even lower resolution structures where they really don't want to give up any information.</div><div><br></div><div>Something like this could be done with cross-validation data after refinement, but the SigmaA determination is much more reliable with more reflections, so if it can be done using all the data before refinement, the results will be clearer.</div><div><br></div><div>Regards,</div><div><br></div><div>Randy Read</div><div><br><div><div>On 6 Oct 2010, at 15:10, Pavel Afonine wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
Hi,<br>
<br>
isn't it better to use all data in refinement and expect that the ML
target will down-weight those reflections that needs to? And if you
have one single reflection at 1A resolution, while the data extends
complete up to 2A resolution, you would use it up to 2A anyway? <br>
Anyway, I hope Randy might comment on this...<br>
<br>
Regardless, as I wrote yesterday I will add this functionality as
soon as I get a chance.<br>
<br>
Pavel.<br>
<br>
<br>
On 10/6/10 6:48 AM, crystallogrphy wrote:
<blockquote cite="mid:AANLkTikZRSEqjJd1rcBKM=U43ZxVzYoZ0+Fn_ieUXtXS@mail.gmail.com" type="cite">Hi, Pavel:<br>
I actually also need this function: sigma vs resolution, because I
want to determine what is the real resolution of my crystal data.
Randy Read and Axel Brunger had a paper talking about it. <br>
<br>
<div class="gmail_quote">
On Wed, Oct 6, 2010 at 12:47 AM, Pavel Afonine <span dir="ltr"><<a moz-do-not-send="true" href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hi Bryan,
<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
how might one start to go about getting phenix to
automatically write out the value of sigma_A vs.
resolution?<br>
<br>
e.g. when making maps, to get that nice table in Randy
Read's SIGMAA program output of ln(sigma_A) vs.
resolution.<br>
</blockquote>
<br>
</div>
easy -:) Simply nobody asked for this so far so it's not
there. I will add it within next few weeks and let you know
once it is available. It's not computed at the moment (we use
different parametrization) but I can reformulate it to get
what you want.<br>
<br>
May I ask you why you need it?<br>
<br>
Thanks!<br>
<font color="#888888">
Pavel.</font>
<div>
<div class="h5"><br>
<br>
_______________________________________________<br>
phenixbb mailing list<br>
<a moz-do-not-send="true" href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a moz-do-not-send="true" href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
</div>
</div>
</blockquote>
</div>
<br>
<style type="text/css">#avg_ls_inline_popup { position:absolute; z-index:9999; padding: 0px 0px; margin-left: 0px; margin-top: 0px; width: 240px; overflow: hidden; word-wrap: break-word; color: black; font-size: 10px; text-align: left; line-height: 13px;}</style>
<pre wrap=""><fieldset class="mimeAttachmentHeader"></fieldset>
_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</div>
_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div>------</div><div>Randy J. Read</div><div>Department of Haematology, University of Cambridge</div><div>Cambridge Institute for Medical Research Tel: + 44 1223 336500</div><div>Wellcome Trust/MRC Building Fax: + 44 1223 336827</div><div>Hills Road E-mail: <a href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a></div><div>Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk</div></span></span>
</div>
<br></div></body></html>