Re: [modeller_usage] non expected atoms !

On 7/25/12 2:29 AM, Anthony Couvreux wrote: > I am trying to model a protein (i.e. a polymerase) with magnesium and a > nucleotide in its active site. The problem is that after calculations, > unless metals and ligand are well localized in the active site , a > meaningless fragment -SCC(N)CO(O) like a cystein- is linked to the last > aminoacid ( a cystein)of my protein.

Sorry, but without seeing all your input files I cannot reproduce your problem, so I can't tell where this extra CYS is coming from. But it looks like an alignment error, such that the '.' in your sequence is aligned with a CYS in your template rather than a ligand.

Ben Webb, Modeller Caretaker