[phenixbb] automr : ensemble on command line

Nathaniel Echols nechols at lbl.gov
Thu Nov 11 16:26:06 PST 2010


On Thu, Nov 11, 2010 at 3:39 PM, Bryan Lepore <bryanlepore at gmail.com> wrote:
> i keep getting this error  :
>
> The number of entries in identity_list ([80.0, 80.0]) needs to be
> the same as the number of entries in ensemble_1.coords (1)
>
> on the command line, i specify the ensemble as :
>
> coords='MR_probe_5_match_to_9.pdb MR_probe_9.pdb' identity='80 80'
>
> it gets picked up like this :
> ...
>  ensembleID = "ensemble_1"
>  copies_to_find = None
>  coords = "MR_probe_5.pdb MR_probe_9.pdb"
>  identity = 80 80
> ...
>
> i tried using quotes or not, and rmsd. i'm using "\" for the shell -
> what am i missing here? any clues to look for?

Pathname parameters that are multiple have to be specified separately
- you can't run them together like that on the command line.  (It's
fine for simpler list parameters like the identity.)  I'd try this
first:

coords="MR_probe_5.pdb" coords="MR_probe_9.pdb" etc.

If that doesn't work, you need to run it from a parameter file
instead.  Alternately, use phenix.ensembler to generate a single
multi-model PDB file.

-Nat



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