i want to use chimera Match->Align feature using the commandline or nogui script (python) to align multiple protein sequences (pdb files) to generate the alignment on MultiAlignViewer and save it as clustal (.aln) file. 

I tried out the python codes posted on the portals but non of them are giving proper alignment.

kindly advice as to what i can do? Is there any commandline available for it?

Thanking You

Sincere User