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
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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