[cctbxbb] CCTBX.XFEL problems with synchrotron stills

Schulz, Eike-Christian eike.schulz at mpsd.mpg.de
Wed Apr 6 06:44:31 PDT 2016

Hi Nick,

Thanks for your help … but unfortunately the problem remains …

Any other idea ?

Best regards


From: <cctbxbb-bounces at phenix-online.org<mailto:cctbxbb-bounces at phenix-online.org>> on behalf of Nicholas Sauter <nksauter at lbl.gov<mailto:nksauter at lbl.gov>>
Reply-To: cctbx mailing list <cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>>
Date: Tuesday 5 April 2016 18:23
To: cctbx mailing list <cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>>
Subject: Re: [cctbxbb] CCTBX.XFEL problems with synchrotron stills


Possibly issuing the command

libtbx.configure xfel

followed by changing to the build directory and


would help sort this out.


Nicholas K. Sauter, Ph. D.
Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
(510) 486-5713

On Tue, Apr 5, 2016 at 1:55 AM, Schulz, Eike-Christian <eike.schulz at mpsd.mpg.de<mailto:eike.schulz at mpsd.mpg.de>> wrote:
Dear all,

I am new to serial crystallography and trying to process still images from a synchrotron source (Pilatus 6M detector) using CCTBX. Obviously the process is not glitch-free and I was hoping to get some help here.

The indexing routine starts, indexes the images correctly and and produces a log file but no .pickle files are created in the results/000/ directory as described in the wiki entry.

I assume that there is a software module that is not properly loaded during the process since I get following error message during indexing:

---------BEGIN Integrate one frame 75 warsaw0048_00075.pickle
EFFECTIVE TILING 0 0 2282 2282
Indexing error: No module named cxi_user

Is there a way to find out if all dependencies are matched ? I suppose CCTBX.XFEL depends on some (specific) python libraries … ?

Or am I completely wrong and the error is something different ?

With best regards


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