Hello!
I've tried to work with the PSSpred standalone copy I've downloaded from your site, since I have to predict a secondary structure of a very large dataset of proteins and it is much more convenient to do it with standalone version. However, the PSSpred script in the PSSpred_v1.tar package has some compilation errors, such as syntax error in lines 244-246 and such as "Unquoted string "fasta" may clash with future reserved word at PSSpred.pl line 218" etc. I've fixed only the syntax errors, not the "Unquoted string... etc. " however script still doesn't work and gives me such an output:
running Psi-blast .....
[blastpgp] WARNING: Unable to open db.pin
[makemat] FATAL ERROR: Unable to open file psitmp.chk
cp: cannot stat `psitmp.mtx': No such file or directory
cannot open file pssm.txt
cannot open file mtx
cannot open file pssm.txt
cannot open file mtx
cannot open file pssm.txt
cannot open file mtx
cannot open file pssm.txt
cannot open file mtx
cannot open file pssm.txt
cannot open file mtx
cannot open file pssm.txt
cannot open file mtx
cannot open file pssm.txt
cannot open file mtx
My question is what am I doing wrong, and what I have to do in order to make the script work ?
Thank you very much,
Alona