<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>Could you double-check the two log files to see whether there was an input error? I agree that the second eLLG result looks more realistic, so I'm wondering if the same information was given about sequence identity and composition of the asymmetric unit. If all the input is the same, that would mean we have a bug to track down.</div><div><br></div><div>On the memory leak question, we'll have to look into which version of gcc is used to compile Phaser with OpenMP support. Unfortunately, there do seem to be problems with older versions of gcc (e.g. the 4.2.1 version distributed with Macs) giving memory leaks. The same code compiled with newer versions of gcc (something like 4.4 or newer, if I remember correctly) works fine.</div><div><br></div><div>Best wishes,</div><div><br></div><div>Randy</div><div><br><div><div>On 19 Nov 2012, at 09:45, Morten Groftehauge wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi guys,<div><br></div><div>I was trying out the new Parallel Phaser (dev-1214) and using a model prepared by Rosetta covering 25% of the total structure (32% identity to the homology model), NCS = 2. 5 models actually but not really relevant since the program spontaneously stopped running after a couple of hours (I love what it's supposed to do though!). My question is about the log however. In the Parallel Phaser log it says:</div>
<div><div><font face="courier new, monospace"> Expected LLG and Resolution Limits</font></div><div><font face="courier new, monospace"> ----------------------------------</font></div><div><font face="courier new, monospace"> Expected LLG target: 120.00</font></div>
<div><font face="courier new, monospace"> Expected LLG achieved: 120.0</font></div><div><font face="courier new, monospace"> Resolution of All Data: 2.38</font></div><div><font face="courier new, monospace"> Resolution limited by eLLG target: 4.83</font></div>
<div><font face="courier new, monospace"> This resolution WILL NOT be used as the default</font></div><div><font face="courier new, monospace"><br></font></div><div><font face="courier new, monospace"> The expected LLG achieved is greater than 120 (eLLG target)</font></div>
<div><br></div><div>but when I tried to recreate that run in the regular Phaser-MR I get this message in the log</div><div><div><font face="courier new, monospace"> Expected LLG and Resolution Limits</font></div><div><font face="courier new, monospace"> ----------------------------------</font></div>
<div><font face="courier new, monospace"> Expected LLG target: 120.00</font></div><div><font face="courier new, monospace"> Expected LLG achieved: 49.7</font></div><div><font face="courier new, monospace"> Resolution of All Data: 2.38</font></div>
<div><font face="courier new, monospace"> Resolution limited by eLLG target: 2.38</font></div><div><font face="courier new, monospace"> This resolution WILL NOT be used as the default</font></div><div><br></div><div>
The expected LLG achieved is less than 60 (half eLLG target)</div><div> FTF rescoring WILL be performed due to low expected LLG signal</div><div> Deep search will be performed from the start</div></div><div><br>
</div><div>I think the second result looks more realistic (unfortunately) but I still don't understand why the difference?</div><div><br></div><div>Cheers,</div><div>Morten</div><div><br></div><div>PS Seems like there's a memory leak in 1214 and 1207 when I run the Phaser step of MR_Rosetta. Does this sound right? Definitely in 1207 but it seems like it's still there in 1214.</div>
<div><br></div>-- <br>Morten K Gr�ftehauge, PhD <div>Pohl Group</div><div>Durham University</div><br>
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div>------</div><div>Randy J. Read</div><div>Department of Haematology, University of Cambridge</div><div>Cambridge Institute for Medical Research Tel: + 44 1223 336500</div><div>Wellcome Trust/MRC Building Fax: + 44 1223 336827</div><div>Hills Road E-mail: <a href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a></div><div>Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk</div></span></span>
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