[phenixbb] XDS data

[Tim Gruene]

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 <tg at shelx.uni-ac.gwdg.de> 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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-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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