[phenixbb] phenix.twin_map_utils gives AttributeError: 'module' object has no attribute 'r_free_flags_params'

[Peter Zwart]

run xtriage, it will compute numbers for you and give twin laws.

P

p.s.

2.0 indicates no twinning, or twinning with a load of other problems ;-)

2008/5/21 Francis E Reyes <Francis.Reyes at colorado.edu>:
> Thanks Peter
>
> I was hoping for testing for perfect merohedral twins. I tried the
> Yeats server http://nihserver.mbi.ucla.edu/Twinning/ and my <I^2>/
> <I>^2 statistics > 2.0 (max is 2.1) . Is that interpreted as untwinned
> then?
>
>
> Thanks
>
> FR
>
> On May 21, 2008, at 10:50 AM, Peter Zwart wrote:
>
>> Try donwloading CCI_APPS. This should be fixed in that release.
>>
>> (your cell and sg has no twin laws though, so you will just get a
>> normal map out of it)
>>
>> P
>>
>> 2008/5/21 Francis E Reyes <Francis.Reyes at colorado.edu>:
>>> chem171-152-dhcp:exptl_fobs_phases_freeR_flags.mtz francisreyes$
>>> phenix.twin_map_utils
>>> xray_data.file=exptl_fobs_phases_freeR_flags.mtz
>>> model=MR.1_pdbset1_refine_007.pdb unit_cell=73.5,73.5,114,90,90,90
>>> space_group="P 41 21 2"
>>>
>>> twin_utils {
>>>  input {
>>>    unit_cell = 73.5 73.5 114 90 90 90
>>>    space_group = "P 41 21 2"
>>>    xray_data {
>>>      file_name = "exptl_fobs_phases_freeR_flags.mtz"
>>>      obs_labels = None
>>>      free_flag = None
>>>    }
>>>    model {
>>>      file_name = "MR.1_pdbset1_refine_007.pdb"
>>>    }
>>>  }
>>>  parameters {
>>>    twinning {
>>>      twin_law = None
>>>      max_delta = 3
>>>    }
>>>  }
>>>  output {
>>>    logfile = "twin_tools.log"
>>>    map_coeffs_root = "MAP_COEFFS"
>>>    obs_and_calc = "obs_and_calc.mtz"
>>>  }
>>> }
>>> Traceback (most recent call last):
>>>  File "/usr/local/phenix-1.3b-rc5/mmtbx/mmtbx/command_line/
>>> twin_map_utils.py", line 7, in <module>
>>>    twin_map_utils.run(args=sys.argv[1:])
>>>  File "/usr/local/phenix-1.3b-rc5/mmtbx/mmtbx/twinning/
>>> twin_map_utils.py", line 256, in run
>>>    tmp_params = utils.r_free_flags_params.extract()
>>> AttributeError: 'module' object has no attribute
>>> 'r_free_flags_params'
>>>
>>>
>>> Any ideas?
>>>
>>> Thanks
>>>
>>> FR
>>>
>>> ---------------------------------------------
>>> Francis Reyes M.Sc.
>>> 215 UCB
>>> University of Colorado at Boulder
>>>
>>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>>>
>>> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>
>>
>>
>> --
>> -----------------------------------------------------------------
>> P.H. Zwart
>> Beamline Scientist
>> Berkeley Center for Structural Biology
>> Lawrence Berkeley National Laboratories
>> 1 Cyclotron Road, Berkeley, CA-94703, USA
>> Cell: 510 289 9246
>> BCSB: http://bcsb.als.lbl.gov
>> PHENIX: http://www.phenix-online.org
>> CCTBX: http://cctbx.sf.net
>> -----------------------------------------------------------------
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>
> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>



-- 
-----------------------------------------------------------------
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB: http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX: http://cctbx.sf.net
-----------------------------------------------------------------