Prime User Manual - ISP
Prime User Manual - ISP
Prime User Manual - ISP
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Appendix B: Environment Variables<br />
HMMER/Pfam<br />
PSP_HMMER_DIR: Location of HMMER distribution (the executables are assumed to be in the<br />
binaries subdirectory). Default is $SCHRODINGER_THIRDPARTY/bin/platform/hmmer,<br />
with the default for SCHRODINGER_THIRDPARTY noted above.<br />
PSP_HMMERDB: Location of Pfam database. Default is $SCHRODINGER_THIRDPARTY/<br />
database/pfam, with the default for SCHRODINGER_THIRDPARTY noted above.<br />
PSIPRED<br />
PSP_PSIPRED_DIR: Location of PSIPRED installation (top level directory containing the bin<br />
and data directories). Default is $SCHRODINGER_THIRDPARTY/bin/platform/psipred,<br />
with the default for SCHRODINGER_THIRDPARTY noted above.<br />
PSP_PSIPRED_DB: Sequence database to use for assembling the PSI-BLAST profile. Allowed<br />
values are nr and pdb. Default: pdb.<br />
SSPRO<br />
PSP_SSPRO_DB: Sequence database to use for assembling the SSPRO profile. Allowed values<br />
are nr and pdb. Default: pdb.<br />
<strong>Prime</strong> 2.1 <strong>User</strong> <strong>Manual</strong>
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