PROFASI  Version 1.5
PROFASI's XML structure file format

While working with PROFASI, it is often convenient to use its own XML structure format to store the structure of protein systems. There are many reasons for introducing this:

All the above issues are addressed by PROFASI's XML structure format. Here is a sample:

<?xml version="1.0"?>
<structure>
<box_length>57.6999999999999957</box_length>
<energy>127.6096792213545825</energy>
<snapshot_time> 0 </snapshot_time>
<profasi_version>1.4.8</profasi_version>
<creation_time>
UTC 2011-Feb-01-17:44:59</creation_time>
<population>
<num_chains>1</num_chains>
<protein id="0">
<sequence>
  * RGKWTYNGITYEGR *
</sequence>
<global_coordinates>
-6.2660000000000000  -5.5970000000000004  -3.4409999999999998
-5.9421299751309578  -5.6627480501613841  -2.0188940261389439
-4.7606256705779826  -6.5864440712716199  -1.7714405175602406
</global_coordinates>
<group index="0" type="ARG">
<coordinates>
2.0942352533962136   2.2435194293934790   -3.1415926535897931
2.1414162734233773   -2.6370843727438729   1.5540134319459780
2.8388317673757530
</coordinates>
</group>
<group index="1" type="GLY">
<coordinates>
1.8356117390315918   0.8009091894546179   -3.1415926535897931

</coordinates>
</group>
<group index="2" type="LYS">
<coordinates>
-2.8358781065452923   2.3615227222406134   -3.1415926535897931
-2.3327310248966375   -2.7777380595288519   -1.8560468038439331
2.8623692260015430   -1.0468954991742636
</coordinates>
</group>

///// MANY MORE NODES /////

<group index="13" type="ARG">
<coordinates>
-1.7226977924681979   -0.2137330785775413   -3.1415926535897931
-2.3538889062619526   -2.7744724772572389   -2.1885416072649102
3.0158907181494810
</coordinates>
</group>
</protein>
</population>
</structure>

The meaning of many of the fields does not need any explanation.

The XML format can be displayed using a web browser like firefox and processed with a plethora of different applications. White space is unimporant.

Since no visualisation program is likely to understand this format yet, we need a way to convert the XML files to PDB files. This is how one does it:

prf_convert abc.xml abc.pdb

The simulation programs can be asked to generate the minimum energy structures in the XML format instad of the PDB format with the following command in the settings file:

snapshot_format 2

Otherwise, one can extract XML structure files from a concluded simulation using extract_snapshot .

See Also
Converting between structure file formats, extract_snapshot

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2