amo rama_map \
-jobname [JOB_NAME] \
-type 0 \
-alpha 5.0 \ # bin size for rama map
-index list_proteins \ # index of all protein IDs
-dirt /path_to_STRIDE_ouput/ \
-output [OUTPUT_DIRECTORY]
Rama map for a single protein
amo rama_map \
-jobname [JOB_NAME] \
-type 1 \
-fastx XXXXX.fasta \
-alpha 5.0 \ # bin size for rama map
-index sec_strucure \ # secondary structure (initially, all 'A')
-dirt /path_to_STRIDE_ouput/ \
-output [OUTPUT_DIRECTORY] \
-hlog # local visualization
