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- ...lysis modules are run through ''pyana'', the Python-implementation of LCLS's analysis framework. Since analysis proceeds directly from the raw data, no ...xfel'' at LCLS is built on five systems: the CSPAD detector, pyana, LCLS’s queuing system, phil, and fundamentally, cctbx.6 KB (1 word) - 00:25, 12 December 2014
- On SLAC's interactive nodes, this takes just over 6 minutes. To avoid problems with r Here, in addition to hot, update and build, there's a command called 'base', which downloads a python and needed packages and c7 KB (1 word) - 23:13, 6 November 2018
- ...ls depend on the ''cctbx.xfel'' installation root directories and the user's shell. To make the ''cctbx.xfel'' analysis modules available to PSDM's ''pyana'',3 KB (1 word) - 19:09, 5 March 2015
- ...pecifies which modules to run. In this case we are running ''cctbx.xfel'''s <code>mod_average</code> module. If we were running multiple modules, we c ...eg/g/cctbx/tutorials/scratch/<b><i><username></i></b> -p 6 -q psanaq -r 2 -s12 KB (1 word) - 17:37, 8 May 2015
- ...><sub>iso</sub> statistics. <i>CC</i><sub>1/2</sub> is defined as Pearson's correlation coefficient between two sets, such that for each unique refl ...mputational resources. Therefore, it is recommended to merge data on SLAC's interactive nodes.12 KB (1 word) - 22:44, 29 September 2014
- ...ot_height: minimum height for a pixel to be considered a maximum (after it's determined to be signal)8 KB (1 word) - 16:54, 18 September 2015
- ...e high-speed readoff. This can be seen in the _sXX_ part of XTC filenames (s for stream). These streams are written to the FFB filesystem located at /re3 KB (1 word) - 23:39, 6 November 2018
- .... For the statistics in cxi.xmerge, this is set to an mtz file with Fcalc's from <em>phenix.fmodel 3u3e.pdb high_resolution=1.78 output.type=real</em>. ...tz_column_F</code> is set to whatever column name contains the reference F's in this case "fmodel".9 KB (1 word) - 17:14, 7 August 2015
- ...the decrypted private key of the newly generated key pair to the ssh-agent's cache. ...remote system, a connection to the agent can be forwarded using the ssh’s <code>-A</code> option. Any ssh-processes on the remote system will now qu6 KB (1 word) - 21:41, 5 February 2014
- val = val:match('^%s*(.-)%s*$') return val:match('^%s*(.-)%s*$')6 KB (1 word) - 10:48, 5 February 2014
- return mw.ustring.format('[[%s|%s]]', page, display) return mw.ustring.format('[[%s]]', page)35 KB (1 word) - 10:48, 5 February 2014
- -- Editors can experiment in this template's sandbox (edit | diff) and testcases (edit) pages. cfg['experiment-blurb-template'] = "Editors can experiment in this template's $1 and $2 pages."18 KB (1 word) - 10:48, 5 February 2014
- nsVals[i] = format('"%s"', val) tinsert(self[tname], format('[[Category:%s|%s]]', cat, sort))17 KB (1 word) - 10:48, 5 February 2014
- To make the ''cctbx.xfel'' analysis modules available to PSDM's ''pyana'',14 KB (1 word) - 17:15, 7 August 2015
- ...u observe lots of variation in your intensities per image per bin, then it's fairly safe to increase max_ct. This has the effect of smoothing things out * It's not clear what's causing the EOFError. However, we should at least check for memory leaks t14 KB (1 word) - 17:27, 11 August 2015
- ...detector geometry and experimental parameters to be present in the image’s header. Generally this consists of detector distance, wavelength, pixel si Usage: cxi.image2pickle [-v] [-c] [-s] [-w wavelength] [-d distance] [-p pixel_size] [-x beam_x] [-y beam_y] [-o11 KB (1 word) - 23:04, 6 November 2018
- -i /reg/d/psdm/cxi/cxi84914/xtc/e157 -q psanacsq -s -p 8 -x 157 -r 16 -t 0 * -s funnel all streams for the run into one node (takes longer, but necessary f22 KB (1 word) - 22:36, 15 September 2014
- ....cfg -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages -x cxi84914 -r 24 -s -q psanacsq -p 6 -i /reg/d/psdm/cxi/cxi84914/xtc/e350 ...sed by the beamline operator to a format usable to cctbx.xfel. First, let's extract some useful information from one of the dark averages:6 KB (1 word) - 18:08, 24 September 2014
- ...echo $effective_params|sed -e "s/anomalous=False/anomalous=True/g"|sed -e "s/anom_/noanom_/g"`1 KB (1 word) - 23:16, 25 August 2014
- -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -s -p 8 -x 239 -r 16 -t 0 -i /reg/d/psdm/cxi/cxi84914/xtc/e240 -q psanacsq -s -p 8 -x 240 -r 16 -t 036 KB (1 word) - 21:55, 6 October 2014
- ...echo $effective_params|sed -e "s/anomalous=False/anomalous=True/g"|sed -e "s/anom_/noanom_/g"`1 KB (1 word) - 20:57, 1 October 2014
- ...+Catalog#psana-ModuleCatalog-ModuleCSPadPixCoords::CSPadNDArrProducer SLAC's module catalog]. If we were running multiple modules, we could chain them ...teraction region to the back the CSPAD detector rail at CXI. Typically it's on the order of between 560 and 580 mm. The beamline operator will provide10 KB (1 word) - 03:43, 19 December 2014
- ...an save the content of the output to any file name - in this tutorial, let's save it to thermolysin.phil.11 KB (1 word) - 19:25, 14 February 2017
- ...in the latest phenix installers. The only missing package is DIALS. Here's how to get ''cctbx.xfel'' configured from an existing Phenix installation.743 B (1 word) - 22:02, 6 November 2018
- ...tion package.] Winter, G., Waterman, D. G., Parkhurst, J. M., Brewster, A. S., Gildea, R. J., Gerstel, M., Fuentes-Montero, L., Vollmar, M., Michels-Cla ...h in serial crystallography with DIALS geometry refinement.] Brewster, A. S., Waterman, D. G., Parkhurst, J. M., Gildea, R. J., Young, I. D., O'Riordan30 KB (1 word) - 00:25, 3 August 2019
- * [[Cppxfel Indexing | Indexing with ''cppxfel'']] - cppxfel's own indexing algorithm, TakeTwo2 KB (1 word) - 12:23, 8 June 2016
- ...rameters, followed by the line <code>COMMANDS</code>, after which the task(s) for ''cppxfel'' to complete are listed. In this case, ''cppxfel'' should <9 KB (1 word) - 23:12, 25 November 2015
- ''cctbx.xfel'''s current native file formats, image pickles and integration pickles, are mai ...he hood these are serialized python dictionaries, but for general users it's sufficient to know that the blob of data consists of name/value pairs. The9 KB (1 word) - 23:10, 6 November 2018
- ...n. ''cctbx.xfel'' uses masks and pedestals deployed into the experiment’s calibration store using the LCLS program calibman [https://confluence.slac. ...tions using powder rings can be done manually using ''cctbx.xfel'' or LCLS's calibman tool [https://confluence.slac.stanford.edu/display/PSDM/Calibratio40 KB (1 word) - 23:55, 18 May 2016
- ...sed -e "s,FS,Flex,g"|sed -e "s,DMIN,$dmin,g"|sed -e "s,NEG,$neg,g"|sed -e "s,TAG,$tag,g"` ...sed -e "s,FS,Flex,g"|sed -e "s,DMIN,$dmin,g"|sed -e "s,NEG,$neg,g"|sed -e "s,TAG,$tag,g"`13 KB (1 word) - 01:00, 25 February 2017
- ...sigma cutoffs are set to 1.5 in scaling and post-refinement steps while it's set to -3.0 so we can include negative values in the merged reflection set.13 KB (1 word) - 20:38, 14 February 2017
- dxtbx.image_average -v -a avg.pickle -m max.pickle -s stddev.pickle -n 64 $data/*.cbf.bz2 ...t for the average, maximum and standard deviation images using -a, -m and -s. -v means verbose output, and we specify 64 cores for averaging using -n.6 KB (1 word) - 00:11, 2 March 2017
- dials.import file.h5 (the h5 will have 1000's of images in it)3 KB (1 word) - 01:48, 18 November 2017
