Hello,
I'm using PyMOL 1.8.6.1 (64 bits) on a Linux distribution (CentOS 7). I
used PyMOL API for CE alignment (protein and ligand) with a reference
(target) protein. Then, I saved the aligned protein and ligand. Input
and output format are mol2. However, I noticed that atomic types from
aromatic ring aren't correct. From the input file, type is 'C.ar' but
becomes 'C.2' in the output file. The right bond type is conserved (C.ar).
So my question is: Is it a bug or an expected behavior ?
Best regards
Célien Jacquemard
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