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.ramalyze phenix.rotalyze phenix.cbetadev phenix.clashscore phenix.reduce (not a validation tool, but it identifies Asn/Gln/His flips) phenix.show_geometry_outliers phenix.real_space_correlation 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 bonds, 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 reported).

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 that). -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]