Rosetta 3.1 Release Manual

Documentation for ca_to_allatom application

Metadata

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

Overview

This is an application intended to aid in building a full-atom mdoel from a low-resolution C-alpha-only trace (such as hand-traced models from cryo-electron microscopy). The input to the protocol includes the initial C-alpha trace and a rigid-body segmentation file, which identifies secondary-structure elements in the initial trace. The protocol is divded into 4 phases: The first two phases may be done in either all-atom or centroid mode. Loop modelling is always done in centroid mode, while all-torsion minimization is always fullatom.

Sample Command Lines

Example 1. Fragment insertion and rigid-body perturbation in fullatom mode (using score13_env_hb), with no sequence-shifting moves. Loop modeling and all-atom relax as usual.
bin/ca_to_allatom.linuxgccrelease \
 -database ~/rosetta_database/ \
 -in:file:s 1cid.pdb \
 -in:file:fullatom \
 -RBSegmentRelax:rb_file 1cid.rbsegs \
 -RBSegmentRelax:rb_scorefxn score13_env_hb \
 -RBSegmentRelax:nrbmoves  250 \
 -RBSegmentRelax:cst_wt    1.0 \
 -RBSegmentRelax:cst_width 4.0 \
 -RBSegmentRelax:skip_seqshift_moves \
 -RBSegmentRelax:helical_movement_params 40.0 1.0 5.0 0.2 \
 -RBSegmentRelax:strand_movement_params 40.0 1.0 1.0 0.2 \
 -score:weights score13_env_hb \
 -loops:strict_loops \
 -loops:random_loop \
 -loops:frag_sizes 9 3 1 \
 -loops:frag_files aa1cid_09_05.200_v1_3.gz aa1cid_03_05.200_v1_3.gz none \
 -loops:build_attempts 10 \
 -loops:remodel quick_ccd \
 -loops:intermedrelax no \
 -loops:refine no \
 -loops:relax fastrelax \
 -relax:fastrelax_repeats 4 \
 -constraints::cst_weight 1.0 \
 -out:nstruct 1 \
 -frag_randomness 2.0

Example 2. Fragment insertion and rigid-body perturbation in centroid mode (using score13_env_hb), with sequence-shifting moves. Loop modeling is done, but no all-atom relax.

bin/ca_to_allatom.linuxgccrelease \
 -database ~/rosetta_database/ \
 -in:file:s 1cid.pdb \
 -in:file:centroid_input \
 -RBSegmentRelax:rb_file 1cid.rbsegs \
 -RBSegmentRelax:rb_scorefxn score5 \
 -RBSegmentRelax:nrbmoves  1000 \
 -RBSegmentRelax:cst_wt    1.0 \
 -RBSegmentRelax:cst_width 4.0 \
 -RBSegmentRelax:helical_movement_params 40.0 1.0 5.0 0.2 \
 -RBSegmentRelax:strand_movement_params 40.0 1.0 1.0 0.2 \
 -score:weights score13_env_hb \
 -loops:strict_loops \
 -loops:random_loop \
 -loops:frag_sizes 9 3 1 \
 -loops:frag_files aa1cid_09_05.200_v1_3.gz aa1cid_03_05.200_v1_3.gz none \
 -loops:remodel quick_ccd \
 -loops:intermedrelax no \
 -loops:refine no \
 -loops:relax no \
 -constraints::cst_weight 1.0 \
 -out:nstruct 1 \
 -frag_randomness 2.0

Example 3. Fragment insertion and rigid-body perturbation in fullatom mode (using score13_env_hb), with sequence-shifting moves. Structures are scored using fit to density. No loop rebuilding

bin/ca_to_allatom.linuxgccrelease \
 -database ~/rosetta_database/ \
 -in:file:s 1cid.pdb \
 -in:file:fullatom \
 -RBSegmentRelax:rb_file 1cid.rbsegs \
 -RBSegmentRelax:rb_scorefxn score13_env_hb \
 -RBSegmentRelax:nrbmoves  25 \
 -RBSegmentRelax:cst_wt    1.0 \
 -RBSegmentRelax:cst_width 5.0 \
 -RBSegmentRelax:helical_movement_params 40.0 1.0 5.0 0.2 \
 -RBSegmentRelax:strand_movement_params 40.0 1.0 1.0 0.2 \
 -score:weights score13_env_hb \
 -edensity:mapfile 1cid_5A.mrc \
 -edensity:whole_structure_allatom_wt 0.02 \
 -edensity:atom_mask 4.0 \
 -edensity:mapreso 5.0 \
 -edensity:grid_spacing 2.0 \
 -out:nstruct 1 \
 -frag_randomness 2.0 \
 -no_lr

Notes

The input PDB -- even though it only needs coordinates for C-alpha atoms -- must have lines for all backbone atoms. These may have coordinates of all 0's, with an occupancy set to -1, or a tool like MaxSprout can be used to find some geometrically reasonable conformation. These coordinates are not used at all by rosetta, but the PDB-reading machinery requires their presence.

The RB segment file (specified with -RBSegmentRelax:rb_file) is as follows:

SEGMENT   1   4   8  E
SEGMENT   2  13  16  E
SEGMENT   3  26  34  E
...
The first column is the word 'SEGMENT', the second is a unique identifier for each segment, the third and fourth a residue range, and the fifth is 'E', 'H', or 'X' depending on secondary structure type (X means compound, for example, if modeling a strand-turn-strand motif as a single element).

The vall file (specified with -loops:vall) is used to generate fragments dynamically, and is included in the Rosetta release.

The app generates bounded constraints from the initial model. The distance at which the constraint score begins to ramp up is given with RBSegmentRelax:cst_width. These constraints may be used throughout the protocol. During the first two steps, the weight is controlled by the flag -RBSegmentRelax:cst_wt, while during looprelax the weight is instead with -constraintscst_weight. Giving the flag '-constrain_relax_to_startcoords' uses tighter constraints during relax.

The default movement parameters may be overridden in the RB segment file: simply add them as an optional 2 or 4 arguments at the end of the corresponding SEGMENT line.

Density-Scoring Options

The options listed below include those specific to the ca_to_allatom application and a selection of common flags that may be useful. If a post-run looprelax is enabled, then the app takes all looprelax and relax specific options. If modelling into density, the app takes all density-fitting options.

Common options:

These flags control whether fullatom or centroid models are used during the first two phases of the protocol (defaults to fullatom). The scorefunction given must agree with this.

The rigid-body segmentation file. See notes above for more info.

The weight and width of the constraints during the first two phases of the protocol. Wider and weaker constraints will produce structures further from the initial CA trace.

The number of moves in phase 1 and phase 2 of the protocol.

The scorefunction used during the first 2 phases of the protocol. If the input pose is fullatom, make sure this is a fullatom function (like score13_env_hb); if centroid make sure it is a centroid function (like score5).

This tell the protocol to skip one of the three move types. Note that if fragment moves are skipped, only 1 fragment insertion is done for each secondary structure element (to build the initial full-atom pose from a C-alpha trace).

The movement parameters, specified as angle-distance pairs. The helical and strand moves have two pairs of these parameters, corresponding to on-axis and off axis movements, while the default case has only one pair. As an example, '-strand_movement_params 40.0 1.0 1.0 0.2' will perturb strands 40 degrees/1A along the strand axis, and 1 degree/0.2A outside the strand axis. These parameters default to 0, so must be specified by the user.

Should we skip looprelax?

Rarely-used options:

If specified, all ligands in the inital trace will not move at all from the starting position

When dynamically choosing fragments in phase 1, this parameter determines how much randomization goes into the search. In general, higher values for this will result in structures further from the starting model.
Generated on Tue Apr 20 07:50:05 2010 for Rosetta Projects by  doxygen 1.5.2

© Copyright Rosetta Commons Member Institutions. For more information, see http://www.rosettacommons.org.