automr : ensemble on command line
dev-572 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? -Bryan
On Thu, Nov 11, 2010 at 3:39 PM, Bryan Lepore
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
On Thu, Nov 11, 2010 at 7:26 PM, Nathaniel Echols
try this first:
coords="MR_probe_5.pdb" coords="MR_probe_9.pdb" etc.
ok, that seems to be working so far, but FYI the webpage says this : If you have an ensemble of search models to search for, then specify it as coords='model_1.pdb model_2.pdb model_3.pdb'
If that doesn't work, you need to run it from a parameter file instead.
same thing as before. anyways, i'll do the other thing.
Alternately, use phenix.ensembler to generate a single multi-model PDB file.
wow, i'll check this out -bryan
On Thu, Nov 11, 2010 at 4:41 PM, Bryan Lepore
ok, that seems to be working so far, but FYI the webpage says this :
If you have an ensemble of search models to search for, then specify it as
coords='model_1.pdb model_2.pdb model_3.pdb'
Oops, that hasn't been true since at least version 1.5 (Tom made some changes to accommodate the GUI). I'll fix the documentation. -Nat
Dear Phenix Developers, A lab member told me that in the latest nightly build (dev-572, for OS X-intel), the GUI appears to override Group ADP mode. Specifically, if one selects "Group ADP refinement mode" as "Group Selection" in the GUI, and reopens the same window later on, the mode seems to have reverted to something else (like two groups per residue). The workaround is to "Edit parameters and run". I have reproduced this problem with my own files. Can you guys reproduce this, or are we missing something here? Best, Engin -- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
On Thu, Nov 11, 2010 at 5:14 PM, Engin Özkan
A lab member told me that in the latest nightly build (dev-572, for OS X-intel), the GUI appears to override Group ADP mode. Specifically, if one selects "Group ADP refinement mode" as "Group Selection" in the GUI, and reopens the same window later on, the mode seems to have reverted to something else (like two groups per residue). The workaround is to "Edit parameters and run". I have reproduced this problem with my own files. Can you guys reproduce this, or are we missing something here?
No, it's definitely a bug - with a one-line fix, fortunately. Thanks for catching this. -Nat
participants (3)
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Bryan Lepore -
Engin Özkan -
Nathaniel Echols