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Phaser–2.1

Index to Documentation

6.1 How to Use XML Output

6.1.1 Generating XML Output
6.1.2 Tags
6.1.3 Error Handing
6.1.4 Logfile Handing

6.2 XML Output Examples

6.2.1 Anisotropy Correction
6.2.2 Cell Content Analysis
6.2.3 Normal Mode Analysis
6.2.4 Automated Molecular Replacement
6.2.5 Automated Experimental Phasing

6. XML Output (for developers)

Phaser can generate XML output from keyword input. XML output should be used in preference to grepping logfiles when incorporating Phaser into automation pipelines. Note that Phaser's python scripting ability is a more powerful way of calling Phaser for automation pipelines.

We would like to hear from developers who wish to incorporate Phaser into automation scripts using the XML functionality cimr-phaser@lists.cam.ac.uk

6.1 How to Use XML Output

6.1.1 Generating XML Output

Phaser outputs an XML file when called with the command line argument -xml followed by the filename for output.

phaser -xml <filename>

If no filename is given, Phaser exits immediately and writes an XML file with filename PHASER.XML describing the error (type="FILE OPENING", message="No XML filename").

6.1.2 Tags

All XML output is wrapped between "phaser" tags with the version number for the Phaser executable and the operating system on which the output was produced as attributes.

<phaser version="2.1" ostype="linux">
  ---All Phaser XML output---
<\phaser>

Names of files are output using the "file" tags with attributes "type" specifying reflections ("HKL") or coordinates ("XYZ") and attribute "format". Currently only "MTZ" and "PDB" formats are output.

<file type="HKL" format="MTZ">filename</file>
<file type="XYZ" format="PDB">filename</file>


Other XML tags are a combination of those suggested by the SPINE consortium and Phaser specific tags. There is no schema. Please refer to the examples.

6.1.3 Error Handling

Successful Phaser execution (not necessarily structure solution!) is reported as

<status>ok</status>

Failure during execution is reported as

<status>error</status>

More information about the type of error is given with

<error>
  <name>ERROR_NAME</name>
  <message>ERROR_MESSAGE</message>
</error>

Allowed values for ERROR_NAME are given in the table below, and specify the type of error. The ERROR_MESSAGE gives more information as to the specific cause of the error.

ERROR_NAME	Failure due to …
SYNTAX	Syntax error in keyword input
INPUT	Input error (e.g. invalid value for an input parameter)
FILE OPENING	Unable to open file (given in ERROR_MESSAGE) for reading or writing.
OUT OF MEMORY	Memory exhaustion
FATAL RUNTIME	Fatal runtime error (e.g. bug in Phaser)
UNHANDLED	Other unhandled fatal error (e.g. bug in libraries)
UNKNOWN	Other error (e.g. bug in compiler)

6.1.4 Logfile Handling

Use the keyword MUTE ON to prevent the writing of the logfile to standard output. Only the XML file and other results files (mtz,pdb) will be produced by Phaser.

6.2 XML Output Examples

Below are example XML output files produced by running the most popular modes of Phaser: anisotropy correction, automated molecular replacement, cell content analysis, normal mode analayis, and SAD phasing.

6.2.1 Anisotropy Correction

Output XML file for anisotropy correction of BETA-BLIP

<phaser version="2.1" ostype="linux">
  <status>ok</status>
  <anisotropy_info>
    <file type="HKL" format="MTZ">beta_blip_ano.mtz</file>
    <eigenB type="1">10.88</eigenB>
    <eigenB type="2">10.88</eigenB>
    <eigenB type="3">-21.76</eigenB>
    <eigenB type="delta">32.64</eigenB>
    <wilson type="K">20.25</wilson>
    <wilson type="B">56.97</wilson>
  </anisotropy_info>
</phaser>


6.2.2 Cell Content Analysis

Output XML file for Cell Content Analysis of BETA-BLIP

<phaser version="2.1" ostype="linux">
  <status>ok</status>
  <cell_content_analysis_info>
    <mw>46375.000000</mw>
    <solution id="0"</cca>
      <Z>1</Z>
      <probVM>0.995130</probVM>
      <VM>2.340743</VM>
    </solution>
  </cell_content_analysis_info>
</phaser>


6.2.3 Normal Mode Analysis

Output XML file for Normal Mode Analysis of beta.pdb (modes 7 and 10, displacement forward only)

<phaser version="2.1" ostype="linux">
  <status>ok</status>
  <normal_modes id="1">
    <file type="XYZ" format="PDB">beta_nma.1.pdb</file>
    <displacement mode="7">0.000000</displacement>
    <displacement mode="10">0.000000</displacement>
  </normal_modes>
  <normal_modes id="2">
    <file type="XYZ" format="PDB">beta_nma.2.pdb</file>
    <displacement mode="7">0.000000</displacement>
    <displacement mode="10">47.306646</displacement>
  </normal_modes>
  <normal_modes id="3">
    <file type="XYZ" format="PDB">beta_nma.3.pdb</file>
    <displacement mode="7">46.881456</displacement>
    <displacement mode="10">0.000000</displacement>
  </normal_modes>
  <normal_modes id="4">
    <file type="XYZ" format="PDB">beta_nma.4.pdb</file>
    <displacement mode="7">46.881456</displacement>
    <displacement mode="10">47.306646</displacement>
  </normal_modes>
  <normal_modes id="5">
    <file type="XYZ" format="PDB">beta_nma.5.pdb</file>
    <displacement mode="7">93.762912</displacement>
    <displacement mode="10">0.000000</displacement>
  </normal_modes>
  <normal_modes id="6">
    <file type="XYZ" format="PDB">beta_nma.6.pdb</file>
    <displacement mode="7">93.762912</displacement>
    <displacement mode="10">47.306646</displacement>
  </normal_modes>
</phaser>


6.2.4 Automated Molecular Replacement

Output XML file for Automated Molecular Replacement of BETA-BLIP

<phaser version="2.1" ostype="linux">
  <status>ok</status>
  <dataset_info>
    <cell>
      <a>75.11</a>
      <b>75.11</b>
      <c>133.31</c>
      <alpha>90</alpha>
      <beta>90</beta>
      <gamma>120</gamma>
    </cell>
    <spacegroup>
      <hall> P 32 2"</hall>
      <number>154</number>
      <lattice>P</lattice>
      <operator id="0">32</operator>
      <operator id="1">2</operator>
      <operator id="2">1</operator>
    </spacegroup>
    <n_symops>6</n_symops>
    <symmetry_operator id="0">
      <aa>1</aa> <ab>0</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>0</ba> <bb>1</bb> <bc>0</bc> <btrans>0</btrans>
      <ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0</ctrans>
    </symmetry_operator>
    <symmetry_operator id="1">
      <aa>0</aa> <ab>1</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>-1</ba> <bb>-1</bb> <bc>0</bc> <btrans>0</btrans>
      <ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0.666667</ctrans>
    </symmetry_operator>
    <symmetry_operator id="2">
      <aa>-1</aa> <ab>-1</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>1</ba> <bb>0</bb> <bc>0</bc> <btrans>0</btrans>
      <ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0.333333</ctrans>
    </symmetry_operator>
    <symmetry_operator id="3">
      <aa>0</aa> <ab>1</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>1</ba> <bb>0</bb> <bc>0</bc> <btrans>0</btrans>
      <ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>0</ctrans>
    </symmetry_operator>
    <symmetry_operator id="4">
      <aa>-1</aa> <ab>-1</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>0</ba> <bb>1</bb> <bc>0</bc> <btrans>0</btrans>
      <ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>0.666667</ctrans>
    </symmetry_operator>
    <symmetry_operator id="5">
      <aa>1</aa> <ab>0</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>-1</ba> <bb>-1</bb> <bc>0</bc> <btrans>0</btrans>
      <ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>0.333333</ctrans>
    </symmetry_operator>
  </dataset_info>
  <solution id="1">
    <file type="HKL" format="MTZ">beta_blip.1.mtz</file>
    <file type="XYZ" format="PDB">beta_blip.1.pdb</file>
    <llg>996.141543</llg>
  </solution>
</phaser>


6.2.5 Automated Experimental Phasing

Output XML file for SAD phasing of insulin

<phaser version="2.1" ostype="linux">
  <status>ok</status>
  <dataset_info>
    <cell>
      <a>78.046</a>
      <b>78.046</b>
      <c>78.046</c>
      <alpha>90</alpha>
      <beta>90</beta>
      <gamma>90</gamma>
    </cell>
    <spacegroup>
      <hall> I 2b 2c 3</hall>
      <number>199</number>
      <lattice>I</lattice>
      <operator id="0">21</operator>
      <operator id="1">3</operator>
      <operator id="2">3</operator>
    </spacegroup>
    <n_symops>24</n_symops>
    <symmetry_operator id="0">
      <aa>1</aa> <ab>0</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>0</ba> <bb>1</bb> <bc>0</bc> <btrans>0</btrans>
      <ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0</ctrans>
    </symmetry_operator>
    <symmetry_operator id="1">
      <aa>-1</aa> <ab>0</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>0</ba> <bb>-1</bb> <bc>0</bc> <btrans>0.5</btrans>
      <ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0</ctrans>
    </symmetry_operator>
    <symmetry_operator id="2">
      <aa>1</aa> <ab>0</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>0</ba> <bb>-1</bb> <bc>0</bc> <btrans>0</btrans>
      <ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>0.5</ctrans>
    </symmetry_operator>
    <symmetry_operator id="3">
      <aa>-1</aa> <ab>0</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>0</ba> <bb>1</bb> <bc>0</bc> <btrans>0.5</btrans>
      <ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>0.5</ctrans>
    </symmetry_operator>
    <symmetry_operator id="4">
      <aa>0</aa> <ab>1</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>0</ba> <bb>0</bb> <bc>1</bc> <btrans>0</btrans>
      <ca>1</ca> <cb>0</cb> <cc>0</cc> <ctrans>0</ctrans>
    </symmetry_operator>
    <symmetry_operator id="5">
      <aa>0</aa> <ab>-1</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>0</ba> <bb>0</bb> <bc>1</bc> <btrans>0.5</btrans>
      <ca>-1</ca> <cb>0</cb> <cc>0</cc> <ctrans>0</ctrans>
    </symmetry_operator>
    <symmetry_operator id="6">
      <aa>0</aa> <ab>-1</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>0</ba> <bb>0</bb> <bc>-1</bc> <btrans>0</btrans>
      <ca>1</ca> <cb>0</cb> <cc>0</cc> <ctrans>0.5</ctrans>
    </symmetry_operator>
    <symmetry_operator id="7">
      <aa>0</aa> <ab>1</ab> <ac>0</ac> <atrans>0</atrans>
      <ba>0</ba> <bb>0</bb> <bc>-1</bc> <btrans>0.5</btrans>
      <ca>-1</ca> <cb>0</cb> <cc>0</cc> <ctrans>0.5</ctrans>
    </symmetry_operator>
    <symmetry_operator id="8">
      <aa>0</aa> <ab>0</ab> <ac>1</ac> <atrans>0</atrans>
      <ba>1</ba> <bb>0</bb> <bc>0</bc> <btrans>0</btrans>
      <ca>0</ca> <cb>1</cb> <cc>0</cc> <ctrans>0</ctrans>
    </symmetry_operator>
    <symmetry_operator id="9">
      <aa>0</aa> <ab>0</ab> <ac>-1</ac> <atrans>0</atrans>
      <ba>1</ba> <bb>0</bb> <bc>0</bc> <btrans>0</btrans>
      <ca>0</ca> <cb>-1</cb> <cc>0</cc> <ctrans>0.5</ctrans>
    </symmetry_operator>
    <symmetry_operator id="10">
      <aa>0</aa> <ab>0</ab> <ac>-1</ac> <atrans>0</atrans>
      <ba>-1</ba> <bb>0</bb> <bc>0</bc> <btrans>0.5</btrans>
      <ca>0</ca> <cb>1</cb> <cc>0</cc> <ctrans>0.5</ctrans>
    </symmetry_operator>
    <symmetry_operator id="11">
      <aa>0</aa> <ab>0</ab> <ac>1</ac> <atrans>0.5</atrans>
      <ba>-1</ba> <bb>0</bb> <bc>0</bc> <btrans>0</btrans>
      <ca>0</ca> <cb>-1</cb> <cc>0</cc> <ctrans>0.5</ctrans>
    </symmetry_operator>
    <symmetry_operator id="12">
      <aa>1</aa> <ab>0</ab> <ac>0</ac> <atrans>0.5</atrans>
      <ba>0</ba> <bb>1</bb> <bc>0</bc> <btrans>0.5</btrans>
      <ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0.5</ctrans>
    </symmetry_operator>
    <symmetry_operator id="13">
      <aa>-1</aa> <ab>0</ab> <ac>0</ac> <atrans>0.5</atrans>
      <ba>0</ba> <bb>-1</bb> <bc>0</bc> <btrans>1</btrans>
      <ca>0</ca> <cb>0</cb> <cc>1</cc> <ctrans>0.5</ctrans>
    </symmetry_operator>
    <symmetry_operator id="14">
      <aa>1</aa> <ab>0</ab> <ac>0</ac> <atrans>0.5</atrans>
      <ba>0</ba> <bb>-1</bb> <bc>0</bc> <btrans>0.5</btrans>
      <ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>1</ctrans>
    </symmetry_operator>
    <symmetry_operator id="15">
      <aa>-1</aa> <ab>0</ab> <ac>0</ac> <atrans>0.5</atrans>
      <ba>0</ba> <bb>1</bb> <bc>0</bc> <btrans>1</btrans>
      <ca>0</ca> <cb>0</cb> <cc>-1</cc> <ctrans>1</ctrans>
    </symmetry_operator>
    <symmetry_operator id="16">
      <aa>0</aa> <ab>1</ab> <ac>0</ac> <atrans>0.5</atrans>
      <ba>0</ba> <bb>0</bb> <bc>1</bc> <btrans>0.5</btrans>
      <ca>1</ca> <cb>0</cb> <cc>0</cc> <ctrans>0.5</ctrans>
    </symmetry_operator>
    <symmetry_operator id="17">
      <aa>0</aa> <ab>-1</ab> <ac>0</ac> <atrans>0.5</atrans>
      <ba>0</ba> <bb>0</bb> <bc>1</bc> <btrans>1</btrans>
      <ca>-1</ca> <cb>0</cb> <cc>0</cc> <ctrans>0.5</ctrans>
    </symmetry_operator>
    <symmetry_operator id="18">
      <aa>0</aa> <ab>-1</ab> <ac>0</ac> <atrans>0.5</atrans>
      <ba>0</ba> <bb>0</bb> <bc>-1</bc> <btrans>0.5</btrans>
      <ca>1</ca> <cb>0</cb> <cc>0</cc> <ctrans>1</ctrans>
    </symmetry_operator>
    <symmetry_operator id="19">
      <aa>0</aa> <ab>1</ab> <ac>0</ac> <atrans>0.5</atrans>
      <ba>0</ba> <bb>0</bb> <bc>-1</bc> <btrans>1</btrans>
      <ca>-1</ca> <cb>0</cb> <cc>0</cc> <ctrans>1</ctrans>
    </symmetry_operator>
    <symmetry_operator id="20">
      <aa>0</aa> <ab>0</ab> <ac>1</ac> <atrans>0.5</atrans>
      <ba>1</ba> <bb>0</bb> <bc>0</bc> <btrans>0.5</btrans>
      <ca>0</ca> <cb>1</cb> <cc>0</cc> <ctrans>0.5</ctrans>
    </symmetry_operator>
    <symmetry_operator id="21">
      <aa>0</aa> <ab>0</ab> <ac>-1</ac> <atrans>0.5</atrans>
      <ba>1</ba> <bb>0</bb> <bc>0</bc> <btrans>0.5</btrans>
      <ca>0</ca> <cb>-1</cb> <cc>0</cc> <ctrans>1</ctrans>
    </symmetry_operator>
    <symmetry_operator id="22">
      <aa>0</aa> <ab>0</ab> <ac>-1</ac> <atrans>0.5</atrans>
      <ba>-1</ba> <bb>0</bb> <bc>0</bc> <btrans>1</btrans>
      <ca>0</ca> <cb>1</cb> <cc>0</cc> <ctrans>1</ctrans>
    </symmetry_operator>
    <symmetry_operator id="23">
      <aa>0</aa> <ab>0</ab> <ac>1</ac> <atrans>1</atrans>
      <ba>-1</ba> <bb>0</bb> <bc>0</bc> <btrans>0.5</btrans>
      <ca>0</ca> <cb>-1</cb> <cc>0</cc> <ctrans>1</ctrans>
    </symmetry_operator>
  </dataset_info>
  <solution_info>
    <file type="XYZ" format="PDB">insulin.pdb</file>
    <file type="HKL" format="MTZ">insulin.mtz</file>
    <llg>81640.054723</llg>
  </solution_info>
</phaser>