Hi, I meant to say that they're included as part of the model for structure factor calculation and in the output PDB file.
Best wishes, Randy On 2 Oct 2012, at 16:05, Francis E Reyes wrote: > 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 ------ 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
