[phenixbb] twin refinement in phenix-1.5-2

jonathan elegheert jonathan.elegheert at ugent.be
Tue Jan 19 09:32:02 PST 2010

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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