PROFASI  Version 1.5
XML configuration file for updates

ProFASi simulation programs offer a way to configure the behaviour of conformational updates to a large extent using an XML configuration file. The configuration file is passed to the program with a command in the settings file or the command line as follows:

config_updates updates.xml

Structure of the update configuration XML file

The top level node should be called config_updates, and it should contain child nodes containing sections for any update you want to configure. The tags corresponding to the update specific nodes should be the name of the individual update, or "all_updates". Here is an example where we increase the probability of choosing backbone angles in residue indices 3,4,5 and 6 by a factor 2.

    <dof id="0:3:b:0"> <weight> 2 </weight> </dof>
    <dof id="0:3:b:1"> <weight> 2 </weight> </dof>
    <dof id="0:4:b:0"> <weight> 2 </weight> </dof>
    <dof id="0:4:b:1"> <weight> 2 </weight> </dof>
    <dof id="0:5:b:0"> <weight> 2 </weight> </dof>
    <dof id="0:5:b:1"> <weight> 2 </weight> </dof>
    <dof id="0:6:b:0"> <weight> 2 </weight> </dof>
    <dof id="0:6:b:1"> <weight> 2 </weight> </dof>

The degrees of freedom for which the behaviour should be changed is identified using the ProFASi DOF identifier strings . The DOF specific nodes above can also be obtained elegantly from a tabular data file using ProFASi's XML template handling capacity (See XML templates: Auto-generate complex XML nodes from tabular data ).

It is also possible to specify a weight for all degrees of freedom in one chain affected by one particular update:

    <chain id="6"> <weight> 10 </weight> </chain>

The effect of the above configuration for updates is that BGS will choose DOFs in chain 6 ten times more often than it would otherwise do. One can use this mechanism to switch off a particular update selectively for a chain, without having to specify all degrees of freedom in the chain explicitly. Note that the chain weights above are multiplicative factor. If a DOF in the chain has previously been given a weight of 3, and the chain is given a weight 10, the two weights are multiplied, and the update chooses that DOF with the multiplied combined weight.

Note also that the above chain wise specification of weights is currently the only working mechanism to control selective application of BGS to a part of the system. The present implementation of BGS in ProFASi works with 4 consecutive residues although this is not a necessity. Sometimes it is not possible to pick the required backbone DOFs from those selected 4 residues, like for instance when there are 2 or more prolines in the range. Putting further constraints on the available range for BGS is technically possible, but would be rather cumbersome book keeping. Since BGS is scheduled for a rewrite relaxing the consecutive residue idea, we refrained from implementing DOF wise constraints on BGS at this stage.

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