PyMOL puts TER records before HETATM residues, even if they are part of the polymer like MSE residues.
Patch attached which considers (ai->flags & cAtomFlag_polymer) instead of (ai->hetatm).
Thomas, can you provide a test case (or cases?) I need a case that will reproduce the problem, and with your fix, corrects it.
fetch 2x19, async=0
save broken.pdb, chain B and resi 49-51
The "broken.pdb" file will have a TER record between 49 and 50, which is wrong.
Patch was applied to SVN repository, commited revision 3994. Thanks Thomas for the patch!
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