[phenixbb] following on the anomalous map

Kay Diederichs kay.diederichs at uni-konstanz.de
Fri Aug 29 03:46:45 PDT 2014

Hi Charles,

> Date: Thu, 28 Aug 2014 09:59:30 -0400
> From: CPMAS Chen <cpmasmit at gmail.com>
> To: Gabor Bunkoczi <gb360 at cam.ac.uk>
> Cc: "PHENIX user mailing list \(phenixbb at phenix-online.org\)"
> 	<phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] following on the anomalous map
> Message-ID:
> 	<CAAU4GKbzA37j=51X4jMOJjq3t4rKW7Jz9+CQrPxO-HN1kFOOiQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> HI, Gabor,
> Thanks for you suggestion.
> I tried this method, it did not give out NO sites for Br.
> why there is apparent anomalous signal and I cannot identify any Br sites?

are you sure that your data processing used the correct parameters?

E.g. in XDS you should definitively be using "FRIEDEL'S_LAW=FALSE". If
you use XSCALE after XDS, it automagically picks up this setting from
XDS_ASCII.HKL i.e. you don't have to specify this again.
If you, by mistake, use FRIEDEL'S_LAW=TRUE, then the large intensity
differences of Friedel pairs will be judged as outliers by XDS, and
these reflections will be rejected - that might lead to featureless maps.

If the anomalous signal is very strong, and the multiplicity is high,
and the Chi^2 values are >1.5, you may also want to use (additionally)
"STRICT_ABSORPTION_CORRECTION=TRUE" . But this is rarely necessary.

There are similar options in other data processing programs. If you mix
and match data processing programs (e.g. XDS integration and aimless
scaling) you have to be careful to have the right settings in all programs.



> As Nat pointed out, other atoms should have very weak anomalous signal
> diffracted at Br absorption peak (3.8e- for Br, versus 0.2e- for the
> sulfurs). In the difference map, I can clearly see some peaks at high sigma
> (> 6), but the anomalous difference map(they are all generated by
> phenix.refine or phenix.maps) is almost featureless, or the peaks has
> no overlaps. The anomalous difference gives the possible place of Br while
> the difference map gives the possible place of the whole ligand, and I
> assume there should be some overlaps between them. Am I right?
> Charles

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