[phenixbb] XDS data

Tim Gruene tg at shelx.uni-ac.gwdg.de
Tue Jan 14 10:24:02 PST 2014

Dear Ryan,

merged data are an old-fashiond left-over from days when disk space was
an issue. It's a shame the PDB only allow merged data, otherwise one
could much more easily retrieve data statistics and anomalous data from
what has been submitted. I would have thought phenix is more
sophisticated by merging internally.

There is also no point in using XSCALE on a single data set, since the
CORRECT step in XDS already scales the data, i.e. XDS_ASCII.HKL is ready
for further treatment without scaling.

If you want to convert XDS output to mtz, I would actually pass on
Clemens Vonrhein's recommendation to use

 pointless->aimless (keyword 'onlymerge'!!!)->truncate

it is a lot more convenient than using XDSCONV.


On 01/14/2014 06:09 PM, Ryan wrote:
> Hi Tim,
> Have you tried using XDSCONV, it will convert the HKL file to an MTZ without
> much trouble. Is there are reason you want the unmerged HKL file rather than
> using XSCALE for scaling and merging? You can choose to leave the data
> unmerged in XSCALE but converting it to an MTZ file will automatically merge
> the data. This is the typical procedure I used for XDS:
> Runs XDS ---> Run XSCALE (makes an .ahkl file) --> Run XDSCONV (makes the
> .mtz file)
> This is the simple script I used for XDSCONV.INP
> OUTPUT_FILE=RKS-II-152_test.hkl  CCP4_I
> INPUT_FILE=RKS-II-152_unmerged.ahkl      !format is XDS_ASCII by default
> Just follow the onscreen instructions after you start XDSCONV. 
> Ryan
> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org
> [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Tim Gruene
> Sent: Tuesday, January 14, 2014 4:43 AM
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] XDS data
> Dear all,
> 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". 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'?
> At the bottom, the message states it would be best to recover the original
> reflection data such as [...] XDS [...].
> This suggests that the original XDS_ASCII.HKL could be used. Is this correct
> in if so, how do I put it into phenix?
> Best,
> Tim
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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