Intro and Install | FAQ | Command Line

FAQ

Q: I try to run one of the *.py scripts and I get "ImportError: No module named open_prospect"
A: Python is unable to find the files needed to bind to OpenProspect.  Make sure the PYTHONPATH environmental variable includes the directory {PREFIX}/lib/python2.3/site-packages/prospect (change python2.x to the version that you have).  This directory should include the file open_prospect.py.


Q: For input files to prospect, what is the difference between an SSP file and an XML file?
A: An SSP file is a secondary structure prediction.   It also included a Point Specific Score Matrix (PSSM) that describe amino acid replacement frequencies as determined by PsiBlast.  An prospect input XML file contains an SSP file inside of it, as well as Indel Frequency Array (IFA) information.  This additional data, also derived from PsiBlast results, has been shown to increase threading alignment accuracy and fold recognition.