典范 wrote: > Could you please tell me how to perform molecular modelling with > multiple chains? I get trouble in preparing the alignment file in > this case.
Modeller should have no problem modeling a multiple-chain system. Simply put the sequences of both chains in your alignment file, and use a chain break character ('/') to separate them. So your template sequence would look something like:
>P1;5fd1 structureX:5fd1:1:A:26:B:::: ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTD SEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMMTSK/ KRRWKKNFIAVSAANRFKKISSSGAL*
Obviously you would change '5fd1' to the actual PDB code of your template structure, and change the starting/ending residue IDs from 1:A and 26:B if necessary.
Ben Webb, Modeller Caretaker