rebuild.pl - Revision history

Edit: /* Options */

2009-07-29T02:37:25Z

Options

Edit: /* Description */

2009-07-29T02:35:14Z

Description

Feig at 14:19, 12 August 2006

2006-08-12T14:19:41Z

New page

__NOTOC__
== Usage ==

<mmtsbToolUsage cmd="rebuild.pl"></mmtsbToolUsage>

== Description ==

Rebuilds an all-atom representation from a low resolution SICHO
protein model based on side chain centers. Either a sequence file
in MONSSTER format (see: <docmark>genseq.pl</docmark>)
and a SICHO chain file with the model coordinates or, if the flag
-pdb is given, a pseudo-PDB file
with side chain centers and optional C-alpha atoms (see: [[genchain.pl]])
are required as arguments. 
The following additional options are available: The -l option can be used
or loop modeling to provide template coordinates from a PDB file and a range
of residues. Only the specified residues are then rebuilt while the template structure
is used to provide coordinates for the remaining residues.
 
The options -r and -o relate to the representation of the
input chain. A different resolution of the lattice projection (other than the
MONSSTER default of 1.45 A) can be specified with -r. With the
option -o it is possible to shift the input chain in lattice units
before the reconstruction. This may be useful for loop modeling when the chain
was shifted as a whole during lattice-based modeling and has to be shifted back
before it can be matched with the original PDB template.
 
No further minimization is done with this script. Subsequent minimizations of the
output generated with this script using [[minCHARMM.pl]]
or [[minAmber.pl]] is recommended to obtain structurally and
energetically improved reconstructions.

== Options ==

; -help : usage information

== Examples ==

<mmtsbToolExample cmd="rebuild.pl" set="/apps/mmtsb/bench/rebuild.pl-test/test1"></mmtsbToolExample>

<mmtsbToolExample cmd="rebuild.pl" set="/apps/mmtsb/bench/rebuild.pl-test/test2"></mmtsbToolExample>

<mmtsbToolExample cmd="rebuild.pl" set="/apps/mmtsb/bench/rebuild.pl-test/test3"></mmtsbToolExample>

@@ Line 8: / Line 8: @@
 Rebuilds an all-atom representation from a low resolution SICHO
 protein model based on side chain centers. Either a sequence file
-in MONSSTER format (see: <docmark>genseq.pl</docmark>)
+in MONSSTER format (see: [[genseq.pl]])
 and a SICHO chain file with the model coordinates or, if the flag
 <B>-pdb</B> is given, a pseudo-PDB file
@@ Line 20: / Line 20: @@
 The options <B>-r</B> and <B>-o</B> relate to the representation of the
 input chain. A different resolution of the lattice projection (other than the
-MONSSTER default of 1.45 A) can be specified with <B>-r</B>. With the
+MONSSTER default of 1.45 &Aring;) can be specified with <B>-r</B>. With the
 option <B>-o</B> it is possible to shift the input chain in lattice units
 before the reconstruction. This may be useful for loop modeling when the chain

@@ Line 34: / Line 34: @@
 ; -help : usage information
+; -pdb file : read chain in PDB format
 == Examples ==