I encountered a weird recent behavior of the command align.
In a script where I use the command
align (PO4 & name OP1+OP2+P), PO4_target
Where PO4 is a selection of O3',O5",P,OP1,OP2 atoms as well as PO4_target
When I run the script with "pymol -c" I get the following
PyMOL>align (PO4 & name OP1+OP2+P), PO4_target
Match: read scoring matrix.
Match: assigning 1 x 1 pairwise scores.
MatchAlign: aligning residues (1 vs 1)...
ExecutiveAlign: 2 atoms aligned.
Executive: RMS = 0.023 (2 to 2 atoms)
The allignment is made only on 2 atoms. (OP1 and OP2)
While, it works if I introduce the command in the graphic window of pymol.
This worked perfectly with earlier versions of pymol.
Best,
Pascal
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