Dear Randy, I just noticed that Phaser 2.5.1 sets the occupancies of attached sugers e.g. NAG, NAM etc. to zero, which caused Buster to crash. Resetting the occupancies to one solved the problem, but other refinement programs may not crash and may cause people unknowingly carrying on zero occupancy sugars. It might be better not to reset the occupancies.
Herman PS: Buster crashing with zero occupancy sugars does not look correct to me either. -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Randy Read Sent: Tuesday, October 02, 2012 4:56 PM To: [email protected] Subject: Re: [ccp4bb] How to output water molecules with Phaser? 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: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
