Dear Randy,
Thank you so much for your reply. I know your concept on water and other
small molecules.
I had changed HETATM to ATOM, but Phaser 2.5.1 still didnot output those
HOH lines, but Phaser 2.1.4 kept all HOH lines starting with ATOM.
Phaser 2.5.1 keeps all other ligands and small molecules if starting
with ATOM. Version 2.5.1 seems to not output only HOH lines.
Best,
Koji
As a deliberate choice, we changed Phaser so that it would omit all HETATM records from the model
used for molecular replacement. This was largely because when extensive water structure was
carried along, it could mess up the molecular replacement calculation. However, if you want
something carried along as part of the model, you should be able to do that simply by changing
"HETATM" to "ATOM " in the lines of the atoms in the PDB file that you want to
keep. I'd suggest being selective in doing this and making sure you're only including the ones
you're deliberately choosing.
The very latest version of Phaser is a bit more clever. One side effect is
that Se-Met residues were left out of the models, but now Phaser recognises the
codes of some modified amino acids and carries them along.
Best wishes,
Randy Read
