On Sun, Jul 31, 2011 at 9:50 AM, Pietro Roversi
I am trying to run phenix.cut_out_density but I seem to be unable to select the map_coeff_labels:
viscount:~/sharpfiles/logfiles/Japanin-ID29-Phaser714.15> phenix.cut_out_density cycle_best_13.pdb eden_flat_55.0pc.mtz << EOF map_coeff_labels="FBshasol SIGFPsha PHIBshasol FOMshasol" EOF
Two problems here: 1) Almost none of the programs in Phenix accept parameters on stdin; the map_coeff_labels parameter needs to go on the command line, or in a parameter file (also specified on the command line). 2) The syntax for map_coeff_labels isn't very intuitive - for the purposes of Phenix, F and SIGF are grouped together as a single array of data. Which ends up looking like this in a parameter file (note the added comma): map_coeff_labels = FBshasol,SIGFPsha PHIBshasol FOMshasol For entering it on the command line, I guess you still need the outer quotes - I'm not sure what this will do to the grouping, however. It's probably easier to edit the parameter file written by the program (by default, cutout_params.eff) and supply that as the sole input. Alternately, it may be more convenient to use the GUI for this, since it will (in theory) select and format the labels correctly. (I don't think I added the interface for this until after 1.7.1, so you'll probably need the latest nightly build.) -Nat