[phenixbb] Phaser not writting out ligands

Nathaniel Echols nechols at lbl.gov
Fri Dec 9 12:01:09 PST 2011

On Fri, Dec 9, 2011 at 11:57 AM, Yarrow Madrona <amadrona at uci.edu> wrote:
> 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.


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