-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Koji,
in case that suits your needs you could do a superposition of the input model (including HETATM) onto the output model. This would move the HETATM's in place. By then deleting the model and merging HETATM's with the output model (e.g. in coot) you've got your result (unless you really want phaser to take the HETATM's scattering into account). Best, Tim On 10/02/2012 05:37 PM, Koji Yonekura wrote: > 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 >> >> >> > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQaxZzUxlJ7aRr7hoRAsbZAJ9qizfHCalh2SBPK8KrlD2y7Z3rTwCg9ZRd u9XXIJjo83vNkIVNq+aWgS0= =xPiv -----END PGP SIGNATURE-----
