[phenixbb] project defaults ncs.params not read or overridden/overwritten by GUI?

Nathaniel Echols NEchols at lbl.gov
Thu Mar 25 11:03:30 PDT 2010

On Mar 25, 2010, at 9:19 AM, Engin Ozkan wrote:
> I remember this. At least from running phenix.refine on command-line, there is a parameter called ncs.find_automatically. It is "True" by default. I remember spending several days trying to change the NCS selections, until I found about this parameter. So, unless you change this parameter to "False", your input is always written over. I am not sure where this might be in the GUI, but it could be the culprit. To see if this is the case, in the Refinement Settings tab, go to All Parameters -> View all settings. There, check under parameters -> refinement -> ncs. You can also find it in the refine_??.eff file, just search for this parameter.

For the record, a related point: if you're used to the command-line version and/or want to confirm that the final parameters are exactly what you intended, you can choose to edit the final .eff file generated by the GUI *before* it actually runs phenix.refine.  Go to Preferences->Refinement, and check the box "Edit parameters before running."  It will open a text editor with the .eff file, and you should be able to change anything in it.

(One word of caution: if you have checked "Add hydrogens automatically", this will be done before you can edit the file, and the PDB file(s) in refinement.input.pdb.file_name will be different than the file(s) shown in the GUI.  This is intentional, but potentially confusing.  It also means that if you restore the job later, the PDB file that will be listed is now the one with hydrogens, not what was originally entered.  Also confusing, but it shouldn't break anything - hopefully the handling of hydrogens will be cleaned up in the next month or two.)


PS. I will see if I can make it a little more obvious what to do about the "Find automatically" option.

Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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