Hello with the following command:
t_coffee -in=input.fasta -method=TMalign_pair,sap_pair -mode=3dcoffee
with the PDB_DIR variable set
with in the file ~/t_coffee/cache/pdb_entry_type.txt: one line per pdb file: <pdb file/name sequence> prot crystal
I obtain the following output along with the alignment:
Multi Core Mode (read): 1 processor(s):
--- Process Method/Library/Aln Msap_pair
xxx Retrieved Msap_pair
--- Process Method/Library/Aln S/scratch/brussel/106/vsc10611/TCOFFEE/GPCRs_A/try.fasta
xxx Retrieved S/scratch/brussel/106/vsc10611/TCOFFEE/GPCRs_A/try.fasta
--- Process Method/Library/Aln Msap_pair
xxx Retrieved Msap_pair
--- Process Method/Library/Aln MTMalign_pair
pdb_pair/TMalign failed:
@»x
pdb_pair/TMalign failed:
@»x
pdb_pair/TMalign failed:
@»x
xxx Retrieved MTMalign_pair
All Methods Retrieved
does this mean the TMalign method didn't work? do you know what this error means?
Thank you for your help.
Kind regards,
Charlotte