Hi again, How about this one ... Traceback (most recent call last): File "/usr/local/phenix-1.6.1-348/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/command_line.py", line 71, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 413, in __init__ self.process_ncs_restraint_groups() File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 672, in process_ncs_restraint_groups log = log) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/ncs/restraints.py", line 306, in from_atom_selections log=log) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/ncs/restraints.py", line 219, in __init__ assert n_ncs > 0 AssertionError Thanks again, Robert
Nope...I did put in the selection..
Below is my params (not default) file:
refinement {
main {
ncs = True
number_of_macro_cycles = 3
optimize_mask = True
}
ncs {
restraint_group {
reference = "chain A and (resseq 218:736 )"
selection = "chain B and (resseq 218:736 )"
selection = "chain C and (resseq 218:736 )"
selection = "chain D and (resseq 218:736 )"
selection = "chain E and (resseq 218:736 )"
selection = "chain F and (resseq 218:736 )"
selection = "chain G and (resseq 218:736 )"
selection = "chain H and (resseq 218:736 )"
selection = "chain I and (resseq 218:736 )"
selection = "chain J and (resseq 218:736 )"
}
}
target_weights {
wxc_scale = 0.02
optimize_wxc = True
optimize_wxu = True
mode = automatic *every_macro_cycle
angles_rmsd_max = 1.5
}
}
On 4/9/10, Ralf W. Grosse-Kunstleve
Hi Robert,
How about this one ... assert n_ncs > 0
Sorry, not a good error message, but I think there's just something funny with your ncs selections: an ncs.restraint_group without any selections. Could you check for this?
Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
It the automatic search turned on? Could you try with refinement.refine.ncs.find_automatically=False (You can add this to the command line or the params file.) Ralf
Sorry for the late reply,
I run using the script, not the GUI...
Thanks for the reply...
Yep, I ran with the find_ncs=False...
That's not the cause...
Thanks,
Robert
On 4/9/10, Ralf W. Grosse-Kunstleve
It the automatic search turned on? Could you try with
refinement.refine.ncs.find_automatically=False
(You can add this to the command line or the params file.)
Ralf
Hi Robert, - are you running phenix.refine using GUI or command line? - what is the exact command you used (if running from command line)? - can you send the .log file? So far I don't know where this error comes from... To say more I need more input from you. Pavel. On 4/9/10 2:00 PM, Robert Ng wrote:
Hi again, How about this one ... Traceback (most recent call last): File "/usr/local/phenix-1.6.1-348/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/command_line.py", line 71, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 413, in __init__ self.process_ncs_restraint_groups() File "/usr/local/phenix-1.6.1-348/phenix/phenix/refinement/driver.py", line 672, in process_ncs_restraint_groups log = log) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/ncs/restraints.py", line 306, in from_atom_selections log=log) File "/usr/local/phenix-1.6.1-348/cctbx_project/mmtbx/ncs/restraints.py", line 219, in __init__ assert n_ncs > 0 AssertionError
Thanks again, Robert _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Pavel Afonine -
Ralf W. Grosse-Kunstleve -
Robert Ng