Prime User Manual - ISP

Table 11.8. Keywords syntax for ska input file (Continued)
Keyword syntax Mode Description
OUTPUT_FILE filename *align*
*scan*
ALISTRUCS_OUTFILE
filename
PSD_THRESHOLD value *align*
*scan*
SSE_MINSIM value *align*
*scan*
SSE_MINLEN value *align*
*scan*
SSE_WINLEN value *align*
*scan*
SWITCH [true | false] *align*
*scan*
Examples
Chapter 11: Command Syntax
The following minimal input file (assumed to be called align.inp) structurally aligns two
protein structures to one another:
QUERY_FILE query.pdb
TEMPLATE template.pdb
File in which to store the structural alignment. Default is
jobname.out.
*align* File in which to store the 3D coordinates of the aligned
structures.
PSD threshold for inclusion in the MSA. Overridden by
RECKLESS.
Minimum Secondary Structural Element (SSE) similarity
for the alignment.
Minimum SSE length for the alignment.
Align only SSE windows of length value.
Carry out global alignment first and then align subwindows
if no similarity was found.
ORDER [seed | psd] *align* psd: order the alignment by PSD to the seed structure.
CLEAN *align* Exclude structures with a PSD < PSD_THRESHOLD from
the alignment.
RECKLESS [true |
false]
*align*
*scan*
Force the alignment of structures even if no similarity is
found.
where query.pdb is the name of the PDB file containing the query structure (the structure to
which we want to align) and template.pdb contains the template structure (the structure we
want to align to the query).
When run using $SCHRODINGER/ska align it should produce the following output:
• align.out—a file containing the structural alignment
• align.log—a log file that contains log information and diagnostics on the run
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