Prime User Manual - ISP

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Chapter 12: Command-Line Utilities
This command runs the structalign utility and returns one aligned file for each
template:
rot-template1.pdb
rot-template2.pdb
rot-template3.pdb
Note: If you encounter a problem involving templates with multiple chains, use the
getpdb utility (see Section D.2.3 of the Maestro User Manual) to extract each
chain into a separate .pdb file, then run structalign again.
4. Import each rot-template.pdb file using the Import button.
Once the files are imported and the aligned templates appear in the Homologs table, select
them all using shift-click or control-click. (Do not select the original structures.) Click Next to
continue to the Edit Alignment step.
12.2 Format Conversion: seqconvert
This utility converts sequences between any permitted input file format and output file format.
This may be useful if autoconversion does not proceed as expected.
Syntax:
$SCHRODINGER/utilities/seqconvert [options]
input-format input_filename output-format output_filename
One use of the seqconvert utility is to convert SSPs produced in Prime to FASTA format with
the following command:
$SCHRODINGER/utilities/seqconvert -inative infile.seq
-ofasta outfile.fasta
Options are described in Table 12.1.
Table 12.1. Keywords for the seqconvert utility
Option Description
-start Read from this sequence in the input file
-end Read to (and including) this sequence in the input file
-h Display usage message
-total Read at most this number of sequences
Prime 2.1 User Manual