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
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 ------------------------------------------------------------------------
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On Feb 10, 2010, at 11:13 PM, Roberto Steiner wrote:
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.
This sounds like a problem with phenix.refine, not the GUI. One possible issue that I discovered yesterday is that there are certain errors that can't be propagated to the GUI - the job crashes, but the GUI still thinks that it's running. These are typically very low-level errors; this is basically impossible to debug without having the data (and it may be system-dependent as well; what platform are you running it on?). The only thing I can suggest in this case is to try running the same refinement on the command line - it may at least print an interpretable error message.
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"
Part of this is probably a bug. Because of the way processes are handled in 1.6, the abort request won't be carried out if the process is simple non-responsive. What does it say on the status bar (the strip at the bottom of the window), and is the little color-cycle widget at the bottom of the right still animated? If the process is still running, it will say so. ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
participants (3)
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Nathaniel Echols -
Pavel Afonine -
Roberto Steiner