Python-based
Hierarchical
ENvironment
for
Integrated
Xtallography
Contents
This program can be used for building a homology model for a target sequence using a template structure and an alignment.
simple_homology_model uses Rosetta, software developed in the Baker laboratory at the University of Washington. See the central installation notes for Rosetta.
simple_homology_model is available from the command line.
The homology model is written out as specified in output.model.
The program first discard all residues from the template structure that are not present in the target and morphs the residue type when they are (this step is performed by Sculptor and is governed by the alignment). The missing segments are detected, a suitable loop modelling setup is devised, which is then fed into Rosetta to do the actual building. For a summary of all keywords with the corresponding defaults, see the Additional information section.
This controls how chain-to-alignment matching is performed. For more information, see the Sculptor documentation.
For each loop, the program backtracks min_residue_margin number of residues on both ends, then checks the distance between bridge residues. If this is shorter than residue_distance * number-of-residues-in-between, than backtracks one residues more on each side, and keeps doing this until the criterion is statisfied, or hits a terminus on either end. After this, it evaluates residue segments that are not assigned for loop modelling and will be kept fixed during the modelling step. Segments shorter than min_edge_segment_length will be discarded at the termini, and shorter than min_intenal_segment_length will be discarded internally, and the surrounding loops joined. It then checks the loop lengths, and stops with an error message if a loop is longer than max_loop_length.
The program runs Rosetta with a kinematic loop closure algorithm (rosetta_loop_closure), as this does not require selected fragments. After the loop is closed, Rosetta can be instructed to run a refinement (rosetta_loop_refinement).
phaser.simple_homology_model \
[ command-line switches ] \
[ PHIL-format parameter files ] \
[ PHIL command-line assignments ] \
[ PDB file ] \
[ alignment file ] \
[ sequence file ]
-h, --help show this help message and exit --show-defaults print PHIL and exit -i, --stdin read PHIL from stdin as well
Everything not starting with a dash('-') is interpreted as a PHIL argument. This can be a PHIL-format file containing parameters, command-line assignment or a file whose type is automatically recognized (based on file extension; structure files and alignment files are recognized automatically).