[modeller_usage] What is the difference in salign_multiple_struc among these 2 conditions

Dear Modellers, I am a bit confused about the utility of auto_overhang=true usage in salign_multiple_struc.py for MSA computation. Even if i don't use this line, result comes the same as _fit files are generated. Same is the case when i don't use this line before computing the alignment writing the result. Alignment files generated are also same in both these cases, both including the sub-optimal alignments.

Please explain me this difference. Is it that auto_overhang option is integrated in salign_multiple_struc.py and is employed automatically without being called for it.

Thanks, Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA