<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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... <div><br></div><div>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... </div><div><br></div><div>If you come up with suggestions for what else to try I would love to hear them :)</div><div><br></div><div>cheers,</div><div>Melania</div><div><br><div><div>On Apr 2, 2012, at 8:45 AM, Mario Sanches wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Jeff,<div><br></div><div>I ran it with XYZ and Individual B-factors refinement. I am sending you the inputs right now so you can do a test. </div><div><br></div><div>Thanks again,</div><div><br></div><div>Mario Sanches</div>
<div><br></div><div><br><div class="gmail_quote">On Mon, Apr 2, 2012 at 11:39 AM, Jeff Headd <span dir="ltr"><<a href="mailto:jjheadd@lbl.gov">jjheadd@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p>Hi Mario,</p><p>Did you run your DEN refinement with optimization? If not, that could explain the behavior. It could also be the default refinement settings. </p><p>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.</p><span class="HOEnZb"><font color="#888888"><p>Jeff</p></font></span><div class="HOEnZb"><div class="h5">
<div class="gmail_quote">On Apr 2, 2012 11:23 AM, "Mario Sanches" <<a href="mailto:mariosan@gmail.com" target="_blank">mariosan@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
An update on the DEN job I was running last Friday:<div><br></div><div>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 :-)</div>
<div><br></div><div>I will be happy to provide the inputs if the developers want to use it on a test.</div><div><br></div><div>Thank you again for your help,</div><div><br></div><div>Mario Sanches<br><br><div class="gmail_quote">
On Fri, Mar 30, 2012 at 11:13 AM, Mario Sanches <span dir="ltr"><<a href="mailto:mariosan@gmail.com" target="_blank">mariosan@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thank you Nat and Jeff for your responses.<div><br></div><div>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.</div>
<div><br></div><div>Thank you again,</div><div><br></div><div>Mario Sanches<div><div><br><br><div class="gmail_quote">On Fri, Mar 30, 2012 at 10:20 AM, Jeff Headd <span dir="ltr"><<a href="mailto:jjheadd@lbl.gov" target="_blank">jjheadd@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p>Hi Mario,</p><p>I've not encountered that bug before, but as Nat said I would suggest trying a more recent installer if you have not.</p><p>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. </p><p>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.</p><p>Thanks,<br>
Jeff</p>
<div class="gmail_quote"><div><div>On Mar 30, 2012 5:42 AM, "Mario Sanches" <<a href="mailto:mariosan@gmail.com" target="_blank">mariosan@gmail.com</a>> wrote:<br type="attribution"></div></div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div>
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.<div>
<br></div><div>Thank you for your inputs.</div><div><br></div><div>Mario Sanches</div><div><br></div><div>___________________________</div><div>Log output final portion:<br><div><br></div><div><p>tardy dynamics:</p><p> number of bodies: 3678</p><p> number of degrees of freedom: 3713</p><p> number of atoms * 3: 38220</p><p> ratio: 0.097 = 1/10.29</p><p> temperature degrees of freedom: cartesian (38220)</p><p> kinetic energy sensitivity to generalized velocities:</p><p> n: 3713</p><p> min: 3.61771e-06</p><p> max: 0.0300001</p><p> mean: 0.00410663</p><p> time step: 0.00100 pico seconds</p><p> velocity scaling: True</p><p> suppressing allowed origin shifts: False</p><p> new target temperature: 2500.00 K</p><p> step= 1 temperature= 2500.0 rmsd=0.0446 r_work=0.3010 r_free=0.3214</p><div><div><br></div>-- <br>Mario Sanches<br>Postdoctoral Researcher<br>Samuel Lunenfeld Research Institute<br>Mount Sinai Hospital<br>
600 University Ave<br>Toronto - Ontario<br>Canada<br>M5G 1X5<br><a href="http://ca.linkedin.com/in/mariosanches" target="_blank">http://ca.linkedin.com/in/mariosanches</a><br>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Mario Sanches<br>Postdoctoral Researcher<br>Samuel Lunenfeld Research Institute<br>Mount Sinai Hospital<br>600 University Ave<br>Toronto - Ontario<br>Canada<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Mario Sanches<br>Postdoctoral Researcher<br>Samuel Lunenfeld Research Institute<br>Mount Sinai Hospital<br>600 University Ave<br>Toronto - Ontario<br>Canada<br>
M5G 1X5<br><a href="http://ca.linkedin.com/in/mariosanches" target="_blank">http://ca.linkedin.com/in/mariosanches</a><br>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Mario Sanches<br>Postdoctoral Researcher<br>Samuel Lunenfeld Research Institute<br>Mount Sinai Hospital<br>600 University Ave<br>Toronto - Ontario<br>Canada<br>
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