On 6/29/12 6:53 AM, Thomas Gaillard wrote: > OK, I was saying "some HETATM records" because of the following > paragraph in MODELLER manual, also mentioning MEX and ABU: > > http://salilab.org/modeller/9.9/manual/node171.html
Oh yes, I'd forgotten about the less common MEX and ABU cases. Yes, those are also mapped, to CYS.
> Because when MODELLER is integrated with other programs, some do not > make the same choice of automatically treating HETATM MSE as ATOM MET > and this can lead to confusion. I think this behaviour should not be > hardcoded.
Makes sense. I'll add an option to turn this off in the next release.
> Additionnally, I think your mapping of MSE SE atom to MET SD atom is slightly > incorrect in the eyes of the PDB standard:
Thanks for catching that - I will fix.
Ben Webb, Modeller Caretaker