[phenixbb] refinement problem

Nathaniel Echols nechols at lbl.gov
Fri Jul 27 07:37:47 PDT 2012


Please see my response to this question from Wednesday:

http://www.phenix-online.org/pipermail/phenixbb/2012-July/018842.html

-Nat

On Fri, Jul 27, 2012 at 6:20 AM, Afshan Begum <afshan490 at yahoo.com> wrote:

> Dear Experts
>
> I am refining my structures in windows mode and every time i got this
> crash message i do not know how to solve this issue? If any one encountered
> this problem kindly suggest me how to solve it. While when i refine with
> refmac the file proceeds smoothly but i want to refinement in phenix due
> to utilize some parameters.
>
> its end like this:
>
>
> Exporting results ==============================
>
> Writing refined structure to PDB file:
>   C:\Documents and Settings\pc user\Desktop\Refine_2\jbu_refine_2.pdb
> n_use            =  7514
> n_use_u_both     =  7514
> n_use_u_iso      =  0
> n_use_u_aniso    =  0
> n_grad_site      =  0
> n_grad_u_iso     =  0
> n_grad_u_aniso   =  0
> n_grad_occupancy =  331
> n_grad_fp        =  0
> n_grad_fdp       =  0
> total number of scatterers =  7514
>
> After that its not produce the map file and gave errore crash mesage.
>
> <module>
> Bus error (Python call stack above)
>                 This crash may be due to a problem in any imported
>                 Python module, including modules which are not part
>                 of the cctbx project. To disable the traps leading
>                 to this message, define these environment variables
>                 (e.g. assign the value 1):
>                     BOOST_ADAPTBX_FPE_DEFAULT
>                     BOOST_ADAPTBX_SIGNALS_DEFAULT
>                 This will NOT solve the problem, just mask it, but
>                 may allow you to proceed in case it is not critical.
>
> Your suggestion highly obliged
>
> I would be very thankful to you
>
> AFSHAN
>
>
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>
>
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