Search results

Create the page "%s" on this wiki! See also the page found with your search.

• Overview
  ...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
• Ha14 installation
  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 c
  7 KB (1 word) - 23:13, 6 November 2018
• Setup
  ...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
• Preparatory steps pyana version
  ...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 -s
  12 KB (1 word) - 17:37, 8 May 2015
• Merging
  ...>_iso statistics. <i>CC</i>_1/2 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
• Phil
  ...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
• Experiment-day guidelines
  ...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 /re
  3 KB (1 word) - 23:39, 6 November 2018
• Resolving an Indexing Ambiguity
  .... 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
• Set up ssh-agent
  ...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 qu
  6 KB (1 word) - 21:41, 5 February 2014
• Arguments
  val = val:match('^%s*(.-)%s*$') return val:match('^%s*(.-)%s*$')
  6 KB (1 word) - 10:48, 5 February 2014
• Documentation
  return mw.ustring.format('[[%s|%s]]', page, display) return mw.ustring.format('[[%s]]', page)
  35 KB (1 word) - 10:48, 5 February 2014
• Documentation/config
  -- 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 $2 pages."
  18 KB (1 word) - 10:48, 5 February 2014
• Message box
  nsVals[i] = format('"%s"', val) tinsert(self[tname], format('[[Category:%s|%s]]', cat, sort))
  17 KB (1 word) - 10:48, 5 February 2014
• Processing L498 thermolysin
  To make the ''cctbx.xfel'' analysis modules available to PSDM's ''pyana'',
  14 KB (1 word) - 17:15, 7 August 2015
• Processing Blog
  ...u observe lots of variation in your intensities per image per bin, then it's fairly safe to increase max_ct. This has the effect of smoothing things out * It's not clear what's causing the EOFError. However, we should at least check for memory leaks t
  14 KB (1 word) - 17:27, 11 August 2015
• Indexing individual stills
  ...detector geometry and experimental parameters to be present in the image’s header. Generally this consists of detector distance, wavelength, pixel si Usage: cxi.image2pickle [-v] [-c] [-s] [-w wavelength] [-d distance] [-p pixel_size] [-x beam_x] [-y beam_y] [-o
  11 KB (1 word) - 23:04, 6 November 2018
• L498 Thermolysin
  -i /reg/d/psdm/cxi/cxi84914/xtc/e157 -q psanacsq -s -p 8 -x 157 -r 16 -t 0 * -s funnel all streams for the run into one node (takes longer, but necessary f
  22 KB (1 word) - 22:36, 15 September 2014
• LB67 Thermolysin
  ....cfg -o /reg/d/psdm/cxi/cxi84914/scratch/$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
• Mergethermo.csh
  ...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
• Gd-Lysozyme
  -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 0
  36 KB (1 word) - 21:55, 6 October 2014