Hello,
loading a pqr (PDB2PQR version 2.1.1) file into pymol 1.7 … 1.9 garbles the
model in some systematic way, whereas PDB2PQR version 1.8 output appears to
be displayed correctly. After superficial inspection I concluded that in
2.1.1 output, columns from (and including) the atom number appear to be
shifted to the right by one position. Indeed, when I apply
sed 's/^ATOM /ATOM/', the so modified 2.1.1 output appears to be displayed
correctly in PyMOL. My question to those familiar with pqr models and the
pymol source: is the sed hack safe as in that it would not distort any
subsequently calculated APBS surfaces?
Best regards.
Wolfram Tempel
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