[phenixbb] refinements settings .eff

Nathaniel Echols nechols at lbl.gov
Tue Oct 11 10:13:53 PDT 2011

On Tue, Oct 11, 2011 at 7:35 AM, Christian Roth
<christian.roth at bbz.uni-leipzig.de> wrote:
> I have done a refinement with an sodium ion. I had generated a phil file for the
> distance restraints to the surrounding water. Now i am not sure if it is
> really there. I removed it and removed the phil from the list in the gui. Now
> phenix complains about no Atom selected and stops.  In the .eff file all
> restraints are incorporated and in I deleted therefore the geometric
> restraints manually from the . eff file. As a consequence an unused parameter
> warning appears about unused parameters or spelling errors in the input file. I
> guess the .eff file.  My default parameter folder is empty. Does phenix load the
> .eff file from the previous run and would it help to remove this?

It will only load the configuration for a previous run if you restore
the job from the project history - but if you click the
"phenix.refine" button in the program list, it will only load whatever
defaults you have set for the project.  A few comments:

- There is some inconsistency in how parameter files are handled in
the GUI: if you add one to the list of input files, they will be
merged into the final parameters and saved to a single .eff file.
This means that when you restore the job configuration, it will
pre-load those parameters from the external file, which won't appear
in the input list.  I'm considering changing this, since it even
confuses me at times.
- The "defaults" directory is no longer the only place to store
default files, and its contents will not necessarily be used.  To add
or remove default files, click "Settings" above the project list, then
click the button labeled "Manage default files".  (This won't actually
delete anything, just eliminate it from the project settings.)
- You can delete those restraint parameters by going to the Settings
menu, then selecting "Geometry restraints"->"Edit geometry

> I dont wanne start a new project just to be in the default configuration mode
> without additional information in the .eff file.

You shouldn't ever need to do this - just remove any default files as
described above, and start phenix.refine fresh instead of restoring a
saved job.  If you're still seeing spurious distance restraint
parameters, that's probably a bug.

> I did this using the gui so I am not sure how to incorporate the  --unused_ok
> command to which may help to convince phenix to process the job.

This is impossible right now - I did not think it necessary because
the GUI will always pre-process all input parameters, and remove
anything it doesn't recognize.  You probably have some truncated
parameters left in the edited .eff file; the error message from
phenix.refine should tell you what these are.


More information about the phenixbb mailing list