phenix.refine & twinning
Can phenix detwin data? I have tried to input the twinning law (l,-k,h) but phenix.refine does not create the appropriate maps and there is no appreciable change in R-factor. I have attached my xtriage and refinement logs. Thanks, Nick
On Mon, Jan 17, 2011 at 11:53 AM, Nicholas Cody Sennett
Can phenix detwin data? I have tried to input the twinning law (l,-k,h) but phenix.refine does not create the appropriate maps and there is no appreciable change in R-factor. I have attached my xtriage and refinement logs.
I can't see any reason why this wouldn't work, but you're right, it's running untwinned ML refinement despite the twin law being set correctly. However, I just tried running the twinned example included in Phenix (the porin-twin dataset, which can be set up as a tutorial from the GUI), and it worked as expected. I'm downloading the latest installer now to double-check, but I doubt it's much different. One possibility is that the REMARK section in the input PDB file is giving conflicting instructions. Could you please run this command and send me the output (off-list, unless you're certain there isn't anything secret in there)? grep "REMARK" /Users/nick/k94e_208/Refine_30M/ligand_revised2-coot-0.pdb thanks, Nat
Hi Nick, I looked through the files you sent and it looks like a bug in phenix.refine (someone reported the same problem before). Sorry about this. I fixed this bug yesterday so please use the latest PHENIX version from nightly builds available after January 17: http://www.phenix-online.org/download/nightly_builds.cgi Meanwhile a quick work-around is to remove a PDB file header (all REMARK 3 records) from input PDB file. Also, to make sure using twinning in refinement will make any difference (at least R-factor wise), run this command: phenix.model_vs_data model.pdb data.mtz and see it it tells the data is twinned. Please let me know if you have any questions. Pavel. On 1/17/11 11:53 AM, Nicholas Cody Sennett wrote:
Can phenix detwin data? I have tried to input the twinning law (l,-k,h) but phenix.refine does not create the appropriate maps and there is no appreciable change in R-factor. I have attached my xtriage and refinement logs.
participants (3)
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Nathaniel Echols -
Nicholas Cody Sennett -
Pavel Afonine