Hi Randy When you say "carried along" are you saying that they are used as part of the molecular replacement search? Or are they temporarily put aside and them simply added to the PDB in frame with the molecular replacement solution (but are not part of the weighted structure factors output in the final mtz)?
F On Oct 2, 2012, at 7:55 AM, Randy Read <rj...@cam.ac.uk> wrote: > 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 > > On 2 Oct 2012, at 15:32, Koji Yonekura wrote: > >> Hi all, >> >> I am using Phaser 2.5.1 for molecular replacement. I like to keep >> tightly bound water molecules (HOH) in the input pdb file. >> Phaser 2.1.4 outputs all HOH lines in the input pdb file to the output >> pdb file, but Phaser 2.5.1 doesnot. >> I am wondering if there is any way to carry input HOH lines to the >> output file with Phaser 2.5.1. >> Best, >> >> Koji > > ------ > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: + 44 1223 336500 > Wellcome Trust/MRC Building Fax: + 44 1223 336827 > Hills Road E-mail: rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
