[phenixbb] phenix.refine frozen

[Pavel Afonine]

Hi Roberto,

I got your email a few days ago and forwarded it to Nat since a part of 
the problem is likely to be related to the GUI somehow.

I need to reproduce this problem to know why it hangs at weights 
calculation step. This is the first time I see it.
Can you send me the data and model and the exact command you used (or 
sequence of clicks)?

What happens if you run the same refinement from the command line?

Pavel.


On 2/10/10 11:13 PM, Roberto Steiner wrote:
> Hi there,
>
> I would appreciate some feedback on the following:
>
> I am playing around with phenix.refine which comes with Phenix distro 
> 1.6-289 for Mac-Intel. When running a normal refinement job
> (ind site + grouped ADPs + ncs+TorsionSimulatedAnnealing) 
> phenix.refine gets stuck after bulk solvent modelling and scaling.
> The last things I see in the log page are:
>
> ====================== bulk solvent modeling and scaling 
> ======================
>
> |--(resolution: 3.50 - 58.55 A; n_refl. = 
> 55140)------------------------------|
> |                                                                     
>         |
> | r_work= 0.2687   r_free= 0.2800   ksol= 0.38   Bsol= 10.09   scale= 
> 1.148   |
> |                                                                     
>         |
> | overall anisotropic scale matrix (Cartesian basis; 
> B11,B22,B33,B12,B13,B23):|
> | (-2.67,-2.67,5.34,0.00,0.00,-0.00); trace/3= 0.00                   
>         |
> |                                                                     
>         |
> | maximum likelihood estimate for coordinate error:   0.41 A          
>         |
> | x-ray target function (ml) for work reflections: 7.216427           
>         |
> |-----------------------------------------------------------------------------|
>
> ========================== Target weights: x-ray data 
> =========================
>
>
>
> and that's it. For completeness, I must report that I changed the 
> defaults of wxc_scale and wxu_scale (but surely that cannot be the 
> problem...). 
> Switching off the TorsionSimAnnealing does not help.
>
> Additionally, if I click on the abort button on the bottom-left of the 
> page nothing happens. On the other hand
> if I click on the abort icon at the top of the page I get the message
> "You are not currently running any calculations. Do you want to close 
> this window?"
> If I say Ok the following message appears:
> "There is at least one process running; are you sure you want to exit 
> before it is finished"
>
> Other tasks (phenix.xtriage for example) seem to run fine. 
>
> Any suggestion?
>
> Best
> Roberto
> ------------------------------------------------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100211/6d0cdb27/attachment-0003.htm>