Engin, it's actually me.. I'm rewriting some parts of phenix.refine, slowly, so some accidental glitches (that were not caught by our test) are possible in nightly builds. Sorry. Pavel On 7/1/13 1:58 PM, Engin Özkan wrote:

For the error you got with dev-1418, I thought I would beat Nat to the punch, and tell you that the ordered_solvent modes have recently changed. So, you just have to go to All parameters -> Ordered solvent, and set the mode.

Engin

On 7/1/13 3:09 PM, Subhani Bandara wrote:

...

Dear all,

I am refining a protein structure at 2.5 A.

After running some refinements with water update option on, I manually added water to some positions and ran without water update option as it removes those water from the sites and show green density around. Then after some refinements like this, I tried to use water update option to add water to some newly appeared density.

When I check the option to update water using dev 1418 version it stops with the following error. Also when not using water update option, refinement statistics got worse when I used 1418 compared to 1.8.2-1309 with refinements using same inputs and options.

R work-0.1988 compared to 0.1920 with 1.8.2-1309 Rfree-0.2623 compared to 0.2490 with 1.8.2-1309

Traceback:

File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/thread_utils.py", line 236, in run

return_value = self._target(self._args, self._kwargs, self._c)

File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py", line 94, in __call__

result = self.target()

File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py", line 73, in __call__

result = self.run()

File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py", line 69, in run

refine_object = self._run(args, callback)

File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py", line 85, in _run

call_back_handler=callback)

File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/command_line.py", line 161, in run

call_back_handler=call_back_handler)

File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/driver.py", line 1630, in run

ncs_manager = self.ncs_manager).result

File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/strategies.py", line 155, in __init__

neutron_refinement2 = self.neutron_refinement2)

File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 26, in __init__

self.__call__()

File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 36, in __call__

self.__getattribute__(method_name)()

File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 106, in run_sol

mc = self.macro_cycle)

File "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py", line 79, in _need_to_run

else: raise RuntimeError("Not a valid mode: %s"%mode)

Thanks in advance for any help

Subhani

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-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 w ph: (650)-498-7111 cell: (650)-862-8563

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