Does anyone know how to run make_fragments.pl script for generating fragment files using only SAM secondary structure prediction program. I am using sam3.5.x86_64 from http://www.soe.ucsc.edu/research/compbio/sam.html but didn't got it work. The SAM package does not include predict-2nd program, but I downloaded from http://users.soe.ucsc.edu/~karplus/predict-2nd/ and it didn't work at all. Could you please tell me how should I generate fragment files using SAM secondary structure prediction only since it is important for membrane_abinitio application.
In our lab, we have to run SAM independently, then make sure the output file is in the correct format by using a cleanup script. Then for running make_fragments:
make_fragments.pl -nosam -samfile -nopsipred -nojufo
This should work
Thanks. Should the SAM be run locally or on server ? I got many RDB files from the SAM server. I choose one of them to run with make_fragments . But when I run the same command I dont get the fragments. Instead it terminates and gives the error. I have attached the file for your consideration.
Should the SAM be run locally or on server for generating secondary structure prediction ? Could please anyone help in this matter ?