2 TRACE
Keyword: automated, tracing, chain
File: trace.txt
Last modified: 5-mar-2007

Menu block "TRACE" contains items, which perform automated model building
and chain tracing.  User has to choose the range of a function
application: working segment, key active or clicked history atoms.

Menu block "TRACE" is loaded with "MAIN_CMDS:load_trace.com".

See also "MAIN_DOC:build/new_struc.txt".

3 GOTO_SKEL
Keyword: GOTO_SKEL

Redraws a previously generated skeleton in order to enable its manual
editing.

3 GOTO_HYB
Keyword: GOTO_HYB

Redraws a previously generated skeleton and the hybrid model in order
to enable the hybrid model manual rebuilding, minimization, refinement
of phasing.

3 GOTO_ALA
Keyword: GOTO_ALA

Redraws the current polya ALA model.

3 RoH_JOBS
Keyword: RoH_JOBS

Robert Huber jobs.

This is a single click function, which combines all steps of automated
model building.  It is not really implemented yet.

Configure it with the "MAIN_CONF:create_roh_jobs.pl".

3 TRC_ORIG
Keyword: TRC_ORIG

Locates adjacent origin(s) of molecule(s).

3 GEN_SKEL
Keyword: GEN_SKEL

Generates skeleton around the current selection with box expanded 15
grid points from the current active map.

3 RE_SKEL
Keyword: RE_SKEL

Re-generates skeleton in the same box as defined baove only at
different contouring level.

3 TRC_SKEL
Keyword: TRC_SKEL

Assignes secoondary structure elements and connections to skeleton.
Secondary structures are yellow, main chain straces green.

3 TRC_HYBR
Keyword: TRC_HYBR

Repeats the "TRC_SKEL" step and builds hybrid model (sp3 fragments)
along the main chain trace.

"MAIN_CMDS:trace_3angl.cmds" macro does it.

3 TRC_ALA
Keyword: TRC_ALA

Build poly alanine model along the hybrid model.

"MAIN_CMDS:trace_chain.cmds" macro does it.

3 TRC_SYMM
Keyword: TRC_SYMM

Moves fragments around applying crystal symmetry operators to position
them into a asymmetric unit.

"MAIN_CMDS:trace_symm_overlaps.cmds" macro does it.

3 TRC_MERG
Keyword: TRC_MERG

Merge overlapping fragments into the best unique trace.

This is still work in progress.

3 TRC_SIDE
Keyword: TRC_SIDE

Trace side chains - find the best residue fitting the density and
geometry constraints.

Currently only amino acid residues are supported.

"MAIN_CMDS:trace_side.cmds" macro does it.