<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Oh yes, I forgot to make one point. If you use data to too-high resolution (where you've collected indices not data, as Keith Wilson would put it), at the least you're wasting significant computer time. By going from 3.5 to 2.8A resolution in the 1bos case, we doubled the amount of data, which is only worth doing if there's real information there. I'm not sure I trust even ML refinement to cope with a significant chunk of data representing pure noise -- the measurement errors would have to be estimated very well, and we would have to trust the refinement procedure to make good use of those measurement errors. If all this doesn't work perfectly, adding data to too-high resolution will introduce errors in your model (being fit to noise) and into your maps. Not to mention the inconvenience that your R-factors will go up!<div><br></div><div>Regards,</div><div><br></div><div>Randy</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>
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_______________________________________________<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>
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