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<title>Using DIALS at Diamond Light Source — DIALS documentation</title>
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<div class="section" id="using-dials-at-diamond-light-source">
<h1>Using DIALS at Diamond Light Source<a class="headerlink" href="#using-dials-at-diamond-light-source" title="Permalink to this headline">¶</a></h1>
<p id="introduction">DIALS is centrally installed on the Linux computer systems at Diamond. You can
load the default version of DIALS by typing at the command line:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ module load dials
</pre></div>
</div>
<p>The default version of DIALS (and xia2, etc.) is usually fixed at the start of
a run, however a more recent nightly build of DIALS may be available:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ module load dials/latest
</pre></div>
</div>
<div class="section" id="tutorials">
<h2>Tutorials<a class="headerlink" href="#tutorials" title="Permalink to this headline">¶</a></h2>
<p>For the following tutorials we suggest using the latest version of DIALS:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ module load dials/latest
</pre></div>
</div>
<p>The thaumatin dataset used in the
<a class="reference internal" href="documentation/tutorials/processing_in_detail_tutorial.html"><span class="doc">Processing in Detail</span></a> is centrally
available on the Diamond filesystem at
<code class="samp docutils literal"><span class="pre">/dls/mx-scratch/dials_tutorial/i04_thaumatin/</span></code>.</p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="documentation/tutorials/processing_in_detail_tutorial.html">Processing in Detail</a></li>
<li class="toctree-l1"><a class="reference internal" href="documentation/tutorials/multi_crystal_analysis.html">Multi-crystal analysis with DIALS and BLEND</a></li>
<li class="toctree-l1"><a class="reference internal" href="documentation/tutorials/metrology_corrections.html">Refining multi-tile detector metrology with DIALS</a></li>
</ul>
</div>
</div>
<div class="section" id="general">
<h2>General<a class="headerlink" href="#general" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="index.html">Main documentation page</a></li>
<li class="toctree-l1"><a class="reference internal" href="documentation/programs/index.html">Program documentation</a></li>
</ul>
</div>
</div>
<div class="section" id="using-dials-with-xia2">
<h2>Using DIALS with xia2<a class="headerlink" href="#using-dials-with-xia2" title="Permalink to this headline">¶</a></h2>
<p>As an alternative to running DIALS directly, support for DIALS has been added
within <a class="reference external" href="https://xia2.github.io/">xia2</a>. You can use <a class="reference external" href="https://xia2.github.io/">xia2</a> just as before, simply replacing
<code class="samp docutils literal"><span class="pre">-2d</span></code>, <code class="samp docutils literal"><span class="pre">-3d</span></code>, etc. with <code class="samp docutils literal"><span class="pre">-dials</span></code>:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ xia2 -dials /dls/mx-scratch/dials_tutorial/i04_thaumatin/
Environment configuration...
XIA2_ROOT => /dls_sw/apps/dials/latest/dials-dev20151124/modules/xia2
XIA2CORE_ROOT => /dls_sw/apps/dials/latest/dials-dev20151124/modules/xia2/core
Python => /dls_sw/apps/dials/latest/dials-dev20151124/build/../base/bin/python2.7
CCTBX => /dls_sw/apps/dials/latest/dials-dev20151124/modules
CCP4 => /dls_sw/apps/ccp4/64/6.5/update19/ccp4-6.5
CLIBD => /dls_sw/apps/ccp4/64/6.5/update19/ccp4-6.5/lib/data
CCP4_SCR => /tmp/tmpPJJ4I7
Working directory: /dls/mx-scratch/rjgildea/tmp/insulin
Free space: 175586.36 GB
Host: cs03r-sc-serv-16
Build: v0.4.0.0-94-gf62dc5d
Contact: [email protected]
XIA2 0.4.0.0
DIALS 1.0-pre-210-gdd8f759
Command line: xia2 -dials /dls/mx-scratch/dials_tutorial/i04_thaumatin/
------------------- Autoindexing SWEEP1 --------------------
All possible indexing solutions:
tP 57.79 57.79 150.01 90.00 90.00 90.00
oC 81.72 81.74 150.02 90.00 90.00 90.00
oP 57.80 57.77 150.01 90.00 90.00 90.00
mC 81.73 81.75 150.03 90.00 89.99 90.00
mP 57.77 57.80 150.02 90.00 90.02 90.00
aP 57.81 57.78 150.03 90.01 89.99 89.99
Indexing solution:
tP 57.79 57.79 150.01 90.00 90.00 90.00
-------------------- Integrating SWEEP1 --------------------
Processed batches 1 to 540
Standard Deviation in pixel range: 0.370000 0.450000
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
"o" => good "%" => ok "!" => bad rmsd
"O" => overloaded "#" => many bad "." => weak
"@" => abandoned
Mosaic spread: 0.066 < 0.066 < 0.066
-------------------- Preparing DEFAULT ---------------------
Likely spacegroups:
P 41 21 2
P 43 21 2
Reindexing to first spacegroup setting: P 41 21 2 (h,k,l)
--------------------- Scaling DEFAULT ----------------------
Resolution limit for NATIVE/SWEEP1: 1.36
--------------------- Scaling DEFAULT ----------------------
Resolution limit for NATIVE/SWEEP1: 1.36
Overall twinning score: 2.02
Your data do not appear twinned
Project: AUTOMATIC
Crystal: DEFAULT
Sequence:
Wavelength name: NATIVE
Wavelength 0.97625
Sweeps:
SWEEP SWEEP1 [WAVELENGTH NATIVE]
TEMPLATE th_8_2_####.cbf
DIRECTORY /dls/mx-scratch/dials_tutorial/i04_thaumatin
IMAGES (USER) 1 to 540
MTZ file: /dls/mx-scratch/rjgildea/tmp/insulin/DEFAULT/NATIVE/SWEEP1/integrate/dials_integrated.mtz
For AUTOMATIC/DEFAULT/NATIVE
High resolution limit 1.36 6.08 1.36
Low resolution limit 50.00 50.00 1.40
Completeness 99.8 99.8 97.8
Multiplicity 5.3 4.9 3.1
I/sigma 12.1 31.7 2.1
Rmerge 0.060 0.025 0.364
Rmeas(I) 0.074 0.031 0.508
Rmeas(I+/-) 0.074 0.031 0.488
Rpim(I) 0.031 0.014 0.272
Rpim(I+/-) 0.042 0.017 0.321
CC half 0.999 0.999 0.826
Wilson B factor 8.873
Anomalous completeness 97.5 100.0 77.3
Anomalous multiplicity 2.6 3.1 1.8
Anomalous correlation -0.001 0.299 -0.024
Anomalous slope 0.960 0.000 0.000
Total observations 292195 3740 12288
Total unique 55487 767 3923
Assuming spacegroup: P 41 21 2
Other likely alternatives are:
P 43 21 2
Unit cell:
57.784 57.784 150.002
90.000 90.000 90.000
mtz format:
Scaled reflections: /dls/mx-scratch/rjgildea/tmp/insulin/DataFiles/AUTOMATIC_DEFAULT_free.mtz
mtz_unmerged format:
Scaled reflections (NATIVE): /dls/mx-scratch/rjgildea/tmp/insulin/DataFiles/AUTOMATIC_DEFAULT_scaled_unmerged.mtz
sca format:
Scaled reflections (NATIVE): /dls/mx-scratch/rjgildea/tmp/insulin/DataFiles/AUTOMATIC_DEFAULT_scaled.sca
sca_unmerged format:
Scaled reflections (NATIVE): /dls/mx-scratch/rjgildea/tmp/insulin/DataFiles/AUTOMATIC_DEFAULT_scaled_unmerged.sca
Processing took 00h 13m 16s
XIA2 used... aimless ccp4 dials pointless xia2
Here are the appropriate citations (BIBTeX in xia-citations.bib.)
(1994) Acta Crystallogr. D 50, 760--763
Evans, Philip (2006) Acta Crystallographica Section D 62, 72--82
Winter, G. (2010) Journal of Applied Crystallography 43
Status: normal termination
</pre></div>
</div>
</div>
<div class="section" id="feedback">
<h2>Feedback<a class="headerlink" href="#feedback" title="Permalink to this headline">¶</a></h2>
<p>If you encounter any problems using DIALS or xia2, or indeed have any other
feedback (positive or negative - we love to hear from you either way),
please contact <a class="reference external" href="mailto:dials-support%40lists.sourceforge.net">dials-support<span>@</span>lists<span>.</span>sourceforge<span>.</span>net</a> or <a class="reference external" href="mailto:xia2.support%40gmail.com">xia2<span>.</span>support<span>@</span>gmail<span>.</span>com</a>
respectively.</p>
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