From: Nathaniel Echols <[email protected]>
To: PHENIX user mailing list <[email protected]>
Sent: Thursday, September 10, 2009 11:52:17 AM
Subject: Re: [phenixbb] Phenix crashes
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.htmI 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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>>
[email protected]>> 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:
[email protected]> Cambridge CB2 0XY, U.K.
www-
>
structmed.cimr.cam.ac.uk>
> _______________________________________________
> phenixbb mailing list
>
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http://www.phenix-online.org/mailman/listinfo/phenixbb-------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
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