[phenixbb] phenix.refine frozen

Roberto Steiner roberto.steiner at kcl.ac.uk
Wed Feb 10 23:13:53 PST 2010

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. =  
| r_work= 0.2687   r_free= 0.2800   ksol= 0.38   Bsol= 10.09   scale=  
1.148   |
| overall anisotropic scale matrix (Cartesian basis;  
| (-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  
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?

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