<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Peter,<div><br></div><div>The RESOLVE database doesn't have RNA+protein in it, nor does it have low-resolution histograms, but you can create a new entry very easily. Here is how:</div><div><br></div><div>1. Find a PDB structure that has the characteristics that you want "refine_1.pdb"</div><div><br></div><div>2. Calculate a map with this model at the resolution you are interested in:</div><div> phenix.pdbtools --f-model high_resolution=5 refine_1.pdb</div><div><br></div><div>3. Generate histograms with phenix.resolve. Here is a script:</div><div><br></div><div><div>#!/bin/csh -f</div><div>phenix.resolve<<EOD</div><div>hklin refine_1.pdb.mtz</div><div>labin FP=FMODEL PHIB=PHIFMODEL</div><div>get_histograms</div><div>no_build</div><div>solvent_content 0.5</div><div>database 5</div><div>mask_cycles 1</div><div>minor_cycles 1</div><div>EOD</div><div><br></div></div><div><div><br></div><div>4. Now the file hist_values.dat will have your histograms:</div><div><br></div><div><div> 5.002693 32.71021 ! resolution Boverall</div><div>1 ! 1=protein 2 = solvent</div><div> 0.10198E-01 1.8145 0.41525E-01 ! a1 a2 a3</div><div> 0.14425E-01 0.46920 0.77521 ! a4 a5 a6</div><div> 0.23653E-06 0.34718E-08 0.0000 ! a7 a8 a9</div><div><br></div><div>2 ! 1=protein 2 = solvent</div><div> 0.27101E-01 6.4460 -0.61802 ! a1 a2 a3</div><div> 0.12788E-01 0.55421 -0.39797E-02 ! a4 a5 a6</div><div> 0.0000 0.0000 0.0000 ! a7 a8 a9</div><div><br></div></div><div><br></div><div>5. Paste the contents of hist_values.dat at the end of $PHENIX/solve_resolve/ext_ref_files/segments/rho.list . NOTE: you need one blank line between sections, and an extra 2 blank lines at the very end of the file...otherwise resolve will give a bad error message.</div><div><br></div><div>6. Now when you run phenix.resolve...say "database 7" and it will use your new histograms. It will write a message in the log file like this:</div><div><br></div><div><div> Histogram DB entry # 7 ("5 14.27721 ! resol")</div><div><br></div><div>which should match what you pasted in to the rho.list file...so you know it took your histograms.</div></div><div><br></div><div>All the best,</div><div>Tom T</div><div><br></div></div><div><br></div><div><br><div><div>On Aug 18, 2009, at 3:10 PM, Peter Grey wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello all,<br><br>I try to solve the structure of RNA and RNA/protein complex at low resolution (5A). Phases come from partial model MR solution. <br>I would really welcome advice about density modification in such cases with RESOLVE.. <br> Does the RESOLVE database of density distributions contain RNA/protein examples ? <br>Can RESOLVE work at low resolution given that histograms profiles are at resolutions from 1.2 A to 4 A ? <br><br>Many thanks for you help,<br><br><br>Peter.<br><br> _______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://www.phenix-online.org/mailman/listinfo/phenixbb<br></blockquote></div><br><div apple-content-edited="true"> <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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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:<a href="http://www.phenix-online.org">www.phenix-online.org</a><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></div></span><br class="Apple-interchange-newline"> </div><br></div></body></html>