[phenixbb] twin refinement in phenix-1.5-2

[Kelly Daughtry]

Thanks Jonathan,
Setting fix_rotamers = false  worked immediately! And makes sense in my head.

Kelly
*******************************************************
Kelly Daughtry
PhD Candidate
Department of Physiology and Biophysics
Boston University School of Medicine
590 Commonwealth Ave
R 390
Boston MA, 02215
(P) 617-358-5548
*******************************************************



On Tue, Jan 19, 2010 at 12:32 PM, jonathan elegheert
<jonathan.elegheert at ugent.be> wrote:
> Hi Kelly,
>
> I encountered the same with later nightlies than 1.5-2 also. The problem is
> the "fix_rotamers = True " command. You have to return it to its default
> value "None".
>
> Apparently, some subroutines like that one don't work with twin_f_lsq
> algorithm. I believe because the fix_rotamers function depends on a map cc
> calculation which also in itself doesn't work with twin_f_lsq.
>
> At least that's my understanding.
>
> Jonathan Elegheert
> PhD student
> Ghent University
>
> Kelly Daughtry wrote:
>>
>> Hello all,
>> I am wondering if anyone has run across this problem and knows how to fix
>> it.
>>
>> I have a twinned dateset and I am using phenix.refine to refine the
>> dataset.
>> I have the full 1.5-2 installation.
>>
>> When I include the twin law (-k, -h, -l) in the refinement, I get this
>> error:
>>
>>  File
>> "/usr/swr/phenix-1.5-2/cctbx_project/mmtbx/twinning/twin_f_model.py",
>> line 1651, in map_coefficients
>>    "m_gradient"
>> AssertionError
>>
>> If I do not include the twin law, I do not get the error and the
>> refinment continues as normal.
>>
>> When I downgraded to Phenix.1.4-3 (full install), And use the same
>> twin law, I am able to run phenix.refine without an error.
>>
>> I have attached my definition file for phenix.1.5-2 amd the log file.
>>
>>
>> Thanks in advance for any help you can provide,
>> Kelly Daughtry
>>
>>
>> *******************************************************
>> Kelly Daughtry
>> PhD Candidate
>> Department of Physiology and Biophysics
>> Boston University School of Medicine
>> 590 Commonwealth Ave
>> R 390
>> Boston MA, 02215
>> (P) 617-358-5548
>> *******************************************************
>> ------------------------------------------------------------------------
>>
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