<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Anastasia,<div><br></div><div>Hmmm...I'm sorry for the trouble! It looks to me as though something failed and that the error message about memory is not the actual problem, as your cell is not big and your resolution is very low.</div><div><br></div><div>Could you possibly send me (<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>, not the list) the exact input files and the cut_out_density.eff parameters file that was generated by this run (or your input script file if you used a script)? I will be happy to figure out what happened if you can do that.</div><div><br></div><div>All the best,</div><div>Tom T</div><div> </div><div><br></div><div><br><div><div>On Aug 25, 2011, at 11:27 AM, Anastasia A Aksyuk wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi everyone,<br>I am trying the phenix.cut_out_density. It fails with the error message below. How can I specify "the bigger version"? or what else could I try?<br><br>Actually, I have a set of scripts using ccp4 programs (from <a href="http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model">http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model</a>) which can do the same thing, but I thought it would be nice to use something simpler. Too bad it fails.<br><br>Thanks,<br>Anastasia<br><br><br>Reading model density histograms from /apps/phenix/phenix-1.7.1-743/solve_resolve/ext_ref_files/segments/rho.list<br>Read total of 6 sets of density functions<br>Sorry, need to increase n_asym_unit_max. Try a bigger version<br><br>***************************************************<br>Sorry, this version does not seem big enough...<br> (Current value of isizeit is 48)<br>You might try increasing "isizeit" by using a bigger version (giant/huge)<br>You might try cutting back the resolution<br>You might try "unlimit" allow full use of memory<br>***************************************************<br><br>resolve exit_info:<br> source_file: /net/longnose/scratch2/phenix/phenix-1.7.1-743/solve_resolve/resolve/need_coarse_grid.cpp<br> source_line: 59<br> status: 13<br>Trying size of ... 96 ...<br>Possibly cresolve size 96 was too big for this machine<br><br>Resolve failed<br><br>Error messages:<br><br><br><br><br>Could not run resolve with size 96<br><br><br>COMMANDS USED:<br>pdb_in_memory<br>no_build<br>mask_cycles 1<br>minor_cycles 0<br>no_build<br> cutout<br> fine_grid<br> no_sort<br>resolution 1000 12.0<br>cell1 15.0 15.0 15.0 90 90 90<br>cutout_center 130.2186526 85.5323180106 9.50263752826<br>padding 5.0<br>cutout_mask 1<br>cutout_sphere 10.0<br>rad_mask 5.0<br><br><br><br>************************************************<br>Resolve error message:<br><br><br><br>Could not run resolve with size 96<br><br><br>************************************************<br><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></div></blockquote></div><br><div>
<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; "><div><div><div><div><div><br>Thomas C. Terwilliger<br>Mail Stop M888<br>Los Alamos National Laboratory<br>Los Alamos, NM 87545<br><br>Tel: 505-667-0072 email: <a href="mailto:terwilliger@LANL.gov">terwilliger@LANL.gov</a><br>Fax: 505-665-3024 SOLVE web site: <a href="http://solve.lanl.gov">http://solve.lanl.gov</a><br>PHENIX web site: http:www.phenix-online.org<br>ISFI Integrated Center for Structure and Function Innovation web site: <a href="http://techcenter.mbi.ucla.edu">http://techcenter.mbi.ucla.edu</a><br>TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB">http://www.doe-mbi.ucla.edu/TB</a></div><div>CBSS Center for Bio-Security Science web site: <a href="http://www.lanl.gov/cbss">http://www.lanl.gov/cbss</a><br><br></div></div></div></div><br></div></span><br class="Apple-interchange-newline">
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