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. Best, Tim 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 FRIEDEL'S_LAW=FALSE !TRUE by default GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 !MERGE=FALSE
Just follow the onscreen instructions after you start XDSCONV.
Ryan
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Tim Gruene Sent: Tuesday, January 14, 2014 4:43 AM To: [email protected] 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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-- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A