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

Hi Mario, Did you run your DEN refinement with optimization? If not, that could explain the behavior. It could also be the default refinement settings. I would be interested in your input files to see why your R values are going up so much, but hopefully with better defaults this won't happen. Jeff On Apr 2, 2012 11:23 AM, "Mario Sanches" wrote:

An update on the DEN job I was running last Friday:

It went to completion. However, the Rwork/Rfree where higher than what I had before (original R + 20%). Since it is stil under development I will not read to much into it and wait for a newer version :-)

I will be happy to provide the inputs if the developers want to use it on a test.

Thank you again for your help,

Mario Sanches

On Fri, Mar 30, 2012 at 11:13 AM, Mario Sanches wrote:

...

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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- 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

-- 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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

I've been having the same problem. No matter what settings I use my final R factors are a lot higher than the starting ones. Using default settings they blow up from 31/32 to 50/60 :/ I've gotten them back down to 35 with cartesian annealing but they are still higher than the starting ones and the maps are not any better. With the torsion annealing I can lower them by lowering the starting temperature but even if I go down to 1000K they are still higher than what I start with. I usually optimize both gamma and weight automatically too... I tried running it with individual sites/individual adp with/and without NCS (trying both cartesian and torsion). I also tried using homologous reference models solved at higher resolution... If you come up with suggestions for what else to try I would love to hear them :) cheers, Melania On Apr 2, 2012, at 8:45 AM, Mario Sanches wrote:

Hi Jeff,

I ran it with XYZ and Individual B-factors refinement. I am sending you the inputs right now so you can do a test.

Thanks again,

Mario Sanches

On Mon, Apr 2, 2012 at 11:39 AM, Jeff Headd wrote: Hi Mario,

Did you run your DEN refinement with optimization? If not, that could explain the behavior. It could also be the default refinement settings.

I would be interested in your input files to see why your R values are going up so much, but hopefully with better defaults this won't happen.

Jeff

On Apr 2, 2012 11:23 AM, "Mario Sanches" wrote: An update on the DEN job I was running last Friday:

It went to completion. However, the Rwork/Rfree where higher than what I had before (original R + 20%). Since it is stil under development I will not read to much into it and wait for a newer version :-)

I will be happy to provide the inputs if the developers want to use it on a test.

Thank you again for your help,

Mario Sanches

On Fri, Mar 30, 2012 at 11:13 AM, Mario Sanches wrote: 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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- 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

-- 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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb