Re: [phenixbb] XDS data

Dear Nat, I won't need to send the header, the first line looks as you expect. FRIEDEL'S_LAW=TRUE in the XDS_ASCII.HKL does not mean that the Friedel pairs are merged (it would, though in XSCALE output in combination with MERGE=TRUE). The former keyword affects the scaling, and both Wolfgang Kabsch and George Sheldrick are of the opinion the scaling gives better results by using twice the number of data without hampering with the data quality by ignoring the anomalous differences. XDS does not have the keyword 'merge', only xscale does, but there is not reason to scale the data twice, as XDS output data are already scaled. I will see how far I get with xscale output, but scientifically it would be beneficial for phenix to allow said XDS format (I agree that shelx hkl-format is not a joy for GUIs). We are using the latest release, version 1.8.4. Cheers, Tim On 01/14/2014 04:53 PM, Nathaniel Echols wrote:

On Tue, Jan 14, 2014 at 4:42 AM, Tim Gruene wrote:

...

I would like to run Phaser-EP through the phenix GUI. When I first uploaded the XDS_ASCII.HKL file, there was an error message about "No valid observed reflections found in this file".

Can you send me the first three lines of the file? My guess is that it looks like this:

!FORMAT=XDS_ASCII MERGE=FALSE FRIEDEL'S_LAW=TRUE

which would be interpreted by our XDS reader as being non-anomalous, even though since it's unmerged there is probably nothing stopping us from using the anomalous data anyway. (I need to double-check this, because I don't understand why it would claim "FRIEDEL'S_LAW=TRUE" if I+ and I- are actually kept separate.) If you instead produce a file that starts like this:

!FORMAT=XDS_ASCII MERGE=TRUE FRIEDEL'S_LAW=FALSE

then it will be accepted by the Phaser-EP GUI.

Subsequently I

...

uploaded an unmerged hklf4 file. The GUI tells me I need to let phenix know about it being hklf4 by appending '=hklf4'. However, when I do so, there is an error message the file did not exist and the Data file line goes red. Where should I correctly append '=hklf4'?

This may simply be a bug. Which version are you using? I had attempted to make the GUI handle SHELX files more sensibly (to the extent that's even possible), but I can't remember how successful I was, and it may have been after version 1.8.4 was released. In general, SHELX format is the least compatible of the supported inputs; it's just missing too much information.

-Nat

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