Re: [phenixbb] DEN refinement is crashing

Thank you Nat and Jeff for your responses. I was using the latest stable PHENIX version but now downloaded the latest nightly build. It seems to be running fine now, even thought he job is still running. I will let you know of the output once it is finished. Thank you again, Mario Sanches On Fri, Mar 30, 2012 at 10:20 AM, Jeff Headd wrote:

Hi Mario,

I've not encountered that bug before, but as Nat said I would suggest trying a more recent installer if you have not.

If you still encounter crashes, could you send me your input files off-list so I could try to replicate the problem here? Everything will be kept confidential.

As an aside, DEN refinement will soon be separated out as its own program, with GUI, to allow for more sensible default parameters and directed control.

Thanks, Jeff On Mar 30, 2012 5:42 AM, "Mario Sanches" wrote:

...

I am running phenix.refine using the graphical interface. Under "global refinement paramerters..." I am selecting "DEN". The problem is that Python crashes all the time, always at the same point (see portion of the log output below). Is it a known bug? Is DEN incompatible with some of the options in refinement? My resolution is 2.9A by the way.

Thank you for your inputs.

Mario Sanches

___________________________ Log output final portion:

tardy dynamics:

number of bodies: 3678

number of degrees of freedom: 3713

number of atoms * 3: 38220

ratio: 0.097 = 1/10.29

temperature degrees of freedom: cartesian (38220)

kinetic energy sensitivity to generalized velocities:

n: 3713

min: 3.61771e-06

max: 0.0300001

mean: 0.00410663

time step: 0.00100 pico seconds

velocity scaling: True

suppressing allowed origin shifts: False

new target temperature: 2500.00 K

step= 1 temperature= 2500.0 rmsd=0.0446 r_work=0.3010 r_free=0.3214

-- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches

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-- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches