[PyMOL] migrating Fe ions and the use of 'morph'

[Emilia C. A. (Emily) <ec...@dr...>]

Hello all.

I'm struggling to comprehend why the morph function, as called using
MacPyMOL version 1.7.6.2, is making iron ions either migrate out of the
active site during the interpolation, or completely absent from the
interpolation.

I call the morph function like so:  morph morphresult, pdb1, pdb2, match=#,
where in place of '#' I have tried all the arguments available to match; if
#=in, then the iron ion in one, two, or three chains of the four chains in
each of pdb1 and pdb2, migrates out of the active site(s) and into some
nonsensical space; if #=like or any other argument, the iron ions do not
appear in the interpolation. Both pdb1 and pdb2 have four chains, and in
each of the chains is an iron ion labeled identically as 'FE'.

Has anyone a recommendation for how to address this?

Emily.

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