Prime User Manual - ISP

Prime User Manual
Chapter 12: Command-Line Utilities
12.1 Multiple Template Alignment: structalign
Chapter 12
If multiple templates are selected in the Find Homologs step, they must be rotated into the
same coordinate reference frame before they can be used. The Align Structures button is the
usual means of performing structural alignment of templates, but the structalign utility can
be run from the command line.
The input files must be in PDB format and the templates in them should consist of single
chains. To use the output files, each must be imported into Find Homologs and selected as one
of the templates, replacing the original, unaligned version.
Syntax:
$SCHRODINGER/utilities/structalign [options] input-files
The input files must be in PDB format. The output file name is generated by adding the prefix
rot- to the input file name.
Options:
-h Print usage message.
-force Force alignment even if structures are not sufficiently similar.
To use structalign from the command line:
1. Obtain the PDB structure file of each template. This can be done easily by clicking on the
sequence name of each template of interest to display it in the Workspace.
2. For each structure, choose Export from the Project menu of the Maestro main window to
save the coordinates of the structure to a file. Select PDB format.
You should now have the following files:
template1.pdb template2.pdb template3.pdb
3. At the command line, enter:
$SCHRODINGER/utilities/structalign template1.pdb template2.pdb
template3.pdb
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