[phenixbb] 1.5.2 and validation

Mark Collins mcollins at convex.hhmi.columbia.edu
Fri Oct 23 06:47:56 PDT 2009


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?

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?

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?

Also it seems that the *twinned crashed the validation when run this way (bug 

Thanks Mark

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