[phenixbb] 1.5.2 and validation
NEchols at lbl.gov
Fri Oct 23 07:17:36 PDT 2009
On Oct 23, 2009, at 6:47 AM, Mark Collins wrote:
> I just installed 1.5.2 and tried it out for a few hours this
> afternoon. Is it
> possible to run the phenix programs from the command line without
> being forced
> to launch the shiney new gui?
All but a few of the programs have command-line versions - the
documentation probably needs to be updated to name these. The
exceptions in 1.5-2 are the reflection file editor and Polygon.
However, the next version will have a command-line version of the
reflection file editor.
The integrated validation tools are also GUI-only but all of the
underlying components have their own commands:
phenix.model_vs_data (which also summarizes geometry statistics from
the other programs)
phenix.reduce (not a validation tool, but it identifies Asn/Gln/His
Except for the last, these are very simple to use. There will be
command-line versions of the GUI validation tools in the next version,
but they really just combine the output of existing programs.
> I have 3 structures I had considered finished by R/Rfree and
> Molprobity. I was
> playing around with polygons (great way to quickly assess the
> structure) and
> found that 2 of the 3 strucutres are "bad" with very low RMSDs for
> angles, chirality, dihedrals and planarity. All were refined with
> phenix 1.3,
> but they are all fairly small ~80-90 residues. So do I need to go
> back and
> revisit these, advice much appreciated?
Actually, there's nothing inherently "bad" about very low geometry
RMSDs, but (at least at moderate-to-high resolution) they can indicate
that you've restrained the geometry too tightly, which can make it
more difficult to refine. If the R-factors, maps, and validation
criteria look good, I don't think you need to worry.
> Also I found that I can edit the validate_0.eff (from phenix/
> project_data/ )
> and run the file from the command line. But is there a way to
> actually change
> keys_to_show and fiters for polygon in the gui?
keys_to_show, yes, but you need to use the separate Polygon program
rather than the main validation GUI, which uses a pre-set list of
keys. The filters can't be changed yet. Again, this will all be
fixed in the next version.
> Also it seems that the *twinned crashed the validation when run this
> way (bug
I was wondering what that error meant. . . You need to specify at
least a maximum or minimum value - although I'm not sure what these
should be for that filter. I think I'll change that error message to
be more informative (it isn't really a "bug", but the GUI doesn't know
Lawrence Berkeley Lab
NEchols at lbl.gov
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