[phenixbb] I seem to be unable to select the map_coeff_labels for phenix.cut_out_density

Nathaniel Echols nechols at lbl.gov
Sun Jul 31 10:32:26 PDT 2011

On Sun, Jul 31, 2011 at 9:50 AM, Pietro Roversi
<pietro.roversi at path.ox.ac.uk> wrote:
> 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"

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.)


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