Re: [modeller_usage] HETATM MSE records

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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