[phenixbb] Phenix crashes

Nathaniel Echols NEchols at lbl.gov
Thu Sep 10 09:52:17 PDT 2009


The parameters changed at some point this year, but the main  
documentation link is still for 1.4-3.  We now have the nightly build  
documentation linked from the download page, e.g.:

http://www.phenix-online.org/documentation/nightlies/1.4-147/automr.htm

I suspect in this case it will be necessary to write a parameter file  
rather than use the command line.  Fortunately, there is a very good  
example of this in the documentation.

On Sep 10, 2009, at 9:44 AM, Randy Read wrote:

> Did you cut and paste the command or retype it?  If that's the exact  
> command, I don't know what would be wrong with the bit  
> "ensemble_1.coords=a1.pdb", but "ensemble_1_copies_to_find" should  
> be "ensemble_1.copies_to_find" and "componenet" should be  
> "component" and "_mass" should be ".mass".  So I wonder if the  
> parser got confused by the other syntax errors?
>
> Regards,
>
> Randy Read
>
> On 10 Sep 2009, at 17:28, r n wrote:
>
>> Hi all
>>
>> I am trying to use phenix.automr to search for two component.
>>
>> Tried command line...
>>
>> phenix.automr data=out.sca ensemble_1.coords=a1.pdb   \
>> ensemble_1.RMS=0.65 ensemble_1_copies_to_find=5   
>> componenet_1_mass=25000   \
>> component_1.component_copies=5  ensemble_2.coords=a2.pdb   \
>> ensemble_2.RMS=0.60 ensemble_2.copies_to_find=5   
>> componenet_2_mass=20000   \
>> component_2.component_copies=5
>>
>> Following errors
>>
>> phenix-installer-1.4-147/phenix-1.4-147/phenix/phenix/command_line/ 
>> automr.py", line 483, in <module>
>>  run_automr=run_automr(args=sys.argv[1:])
>> phenix-installer-1.4-147/phenix-1.4-147/phenix/phenix/autosol/ 
>> wizard_command_line.py", line 1237, in Sorry
>>     raise AssertionError,e
>> AssertionError: Sorry, unknown file or keyword:  
>> ensemble_1.coords=a1.pdb
>>
>> Not sure , What is wrong in my command?
>>
>> Also try to use the Gui, but in automr gui only seen option for  
>> data file , not for model? May I am
>> missing something?
>>
>> Thanks
>>
>>
>>
>>
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>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
> ------
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research      Tel: + 44 1223 336500
> Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
> Hills Road                                    E-mail: rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.                       www- 
> structmed.cimr.cam.ac.uk
>
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-------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
NEchols at lbl.gov






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