On Fri, Dec 9, 2011 at 11:57 AM, Yarrow Madrona
I am having trouble with Phaser not writing out my ligands (HEME and small molecule) to it's output PDB even though they are in the input PDB. I am running through the GUI using Phenix version 1.7.3-921. Phenix refine recognizes HEME from the CCP4 library I think so I am not sure why I at least do not get a HEME in the output PDB. Thanks for your help.
Phaser ignores anything named HETATM - the original reason being to throw out water molecules (which should never be included in an MR model). I think this limitation may be removed once it is switched to using the same PDB parser as phenix.refine et al., but you can get around it for now by changing HETATM to ATOM, e.g.: sed 's/HETATM/ATOM /;' model.pdb > model2.pdb PS. please update to the latest build, we fixed a few more bugs after 921. -Nat