Rosetta 3.1 Release Manual

Documentation for loops_from_density application

Metadata

Last edited 6/26/09. Code and documentation by Frank DiMaio dimaio@u.washington.edu.

Overview

This is a simple routine aimed at creating loopfiles for remodelling structures into density. It finds the regions of the structure with worst local fit to density, and rebuilds them, limiting how far into secondary structure elements are rebuilt.

Additionally, the loopfile contains the per-residue fit-to-density scores for a more detailed view of the structure's fit.

Sample Command Line

Given the model 1cid.pdb and the density map 1cid_5A.mrc, the following command creates a loopfile (1cid.loopfile) for remodelling the worst-fitting regions. It will not rebuild more than 2 residues into a strand, but may rebuild arbitrarily far into a helix.

bin/loops_from_density.linuxgccrelease \
 -database ../rosetta_database/ \
 -in::file::s 1cid.pdb \
 -edensity::mapfile 1cid_5A.mrc \
 -edensity::sliding_window 9 \
 -edensity::mapreso 5.0 \
 -edensity::grid_spacing 1.0 \
 -max_helix_melt -1 \
 -max_strand_melt 2 \
 -frac_loop 0.3

Density-Scoring Options

In general, there are only 4 options that are useful to the protocol's output:

• -frac_loop -- the fraction of the structure we want to rebuild (the # of residues rebuilt will not be exactly this fraction, but aim for this value)
• -max_strand_melt -- the maximum distance to rebuild into a strand (-1 means unlimited)
• -max_helix_melt -- the maximum distance to rebuild into a helix (-1 means unlimited)
• -edensity:sliding_window -- compute local correlation scores using this window width

The fit-to-density options -mapfile, -mapreso, -gridspacing, and -atom_mask operate as expected; all others are ignored.

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