Re: [phenixbb] Table 1 stastics

Dear all, I just want to point out that one possible source of discrepancy between I/sigma reported by a data processing program, and I/sigma reported by a program that uses the relevant cctbx routine is the following: that cctbx routine calculates the variance of merged data as max("internal variance", "external variance") which is different from what the data processing programs do (they calculate the "internal variance" - I hope I didn't get it the wrong way round). SHELXC and SHELXL also calculate the variance of the merged data like the data processing programs do. I dislike this "feature" of cctbx but I do not know if phenix.table_one actually uses this routine for this purpose. thanks, Kay P.S. you can find the discussion over at the cctbx mailing list; see e.g. http://phenix-online.org/pipermail/cctbxbb/2012-September/000530.html and other posts. On 10/18/2012 09:08 PM, [email protected] wrote:

Date: Thu, 18 Oct 2012 08:07:44 -0700 From: Nathaniel Echols To: PHENIX user mailing list Subject: Re: [phenixbb] Table 1 stastics Message-ID: Content-Type: text/plain; charset=ISO-8859-1

On Thu, Oct 18, 2012 at 7:53 AM, Andrew Waight wrote:

...

Thanks for Phenix! Anyway quick question, I tried out the "generate Table1" utility for fun and noticed that my I/SigI and completeness do not match what is found in my XSCALE file. ... How does Phenix compute these parameters? Obviously my I/sigI has gotten much better (1.59 versus 0.85) but the scaling statistics should be the correct ones.

It computes these statistics directly from the reflection data you provide, not the log file. (The reasoning being that since these are the data that Phenix actually uses, the statistics calculated from them are more accurate and relevant than whatever the scaling program thinks.) My guess is that some of the internal processing accounts for the difference - could you please send me the data file?

FYI, the plan for the future is to recalculate all of these statistics from unmerged data rather than rely on parsing data processing logfiles, which obey no standard format and are subject to change without notice.

-Nat

-- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [email protected] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".