Prime User Manual - ISP

Chapter 6: Fold Recognition
potentially meaningful (E-value under 1) family identification is found, it may help you select
different or additional seed templates to bring forward to Build Backbone.
To view a template colored by secondary structure, click the check box in the V (Visualization)
column. The template appears in the sequence viewer, and its secondary structure can be
compared to the SSP profile of the query.
Note: The query-template “alignments” that can be visualized in this step are provided only
as a guide in identifying seed templates. Gaps or other unfavorable features will not
affect the quality of the models built using these templates.
6.4 Evaluating Templates
To make use of the seed templates to build a model, they must first be evaluated for their suitability
for comparative modeling. The evaluation is done with the use of two scripts. The
process involves running an alignment for each template, then running the script to do the evaluation.
The first step is to export the SSPs in CASP format (or copy them from the working directory
so that they have a .casp extension). It is recommended that you use both SSPs.
For each template that you want to use, run the alignment script as follows:
$SCHRODINGER/run -FROM psp CMAlign.pl target template seqFile sspFiles
The arguments for this command are described in Table 6.1.
Table 6.1. Arguments for the CMAlign.pl script.
Argument Description
target Name of the query sequence.
template Name of the template, as shown in the Search table of the Fold Recognition step,
including any underscore characters.
seqFile Target sequence file.
sspFiles CASP formatted secondary structure prediction files (.casp), blank-separated.
The alignments are stored in the subdirectory CMAlign. Once you have run CMAlign.pl for
each of the desired templates, you can run the evaluation script:
cd CMAlign
$SCHRODINGER/run -FROM psp checkAlign.pl target
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