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

Francis E Reyes Francis.Reyes at Colorado.EDU
Wed May 21 09:56:53 PDT 2008


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
>>
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>
>
>
> -- 
> -----------------------------------------------------------------
> 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
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---------------------------------------------
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




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