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<p class="MsoNormal">Hi All,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have run phenix.resolve_cryo_em using half maps at 7.5 A resolution (the postprocessed map is at 7.1 A) and I just wanted to clarify a couple of things (I have pasted the end of the logfile below this message). I set the resolution to
7.52 A but didn’t supply a resolution for density modification – it seems to have chosen a value of 5.671 A
<o:p></o:p></p>
<p class="MsoNormal">(1) It states “Estimated improvement of -0.450 A to d_min(FSCref=0.5): 6.628 A” suggesting to me that it agrees with the postprocessed resolution. Is this the value of 7.08 on this line: “FSCref=0.5: 7.08 6.69 6.63”?<o:p></o:p></p>
<p class="MsoNormal">(2) I understand that the actual process of real space refinement doesn’t care about the resolution of the map, but you need to supply it to get meaningful CC values. So my question is what resolution should I supply to RSR if I use the
density modified map?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I realise that a value of “-0.450 A” is at the upper end of what to expect from density improvement, but I can report that the DM map does look noticeably better than the postprocessed map, especially in regions that are less well defined.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Many thanks in advance for any advice<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Dave Lawson<o:p></o:p></p>
<p class="MsoNormal">-----------------------------------<o:p></o:p></p>
<p class="MsoNormal">d-values (A)<o:p></o:p></p>
<p class="MsoNormal">where<o:p></o:p></p>
<p class="MsoNormal">FSCref=0.5: 7.08 6.69 6.63<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Estimated improvement in d_cc_star=0.5: -0.450 A<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">This is new current best working_map_coeffs_info. Estimated<o:p></o:p></p>
<p class="MsoNormal">improvement of -0.450 A to d_min(FSCref=0.5): 6.628 A<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Done testing....R-value: 0.530 Try: 1 ['database 5', 'resolution: 5.67 ', 'dm_resolution: 5.67 ', 'density_modify_unsharpened_maps:False', 'apply_cc_star:True', 'b_iso: None A**2']<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best density modification cycle 1 is try 1 with<o:p></o:p></p>
<p class="MsoNormal">Methods used: ['database 5', 'resolution: 5.67 ', 'dm_resolution: 5.67 ', 'density_modify_unsharpened_maps:False', 'apply_cc_star:True', 'b_iso: None A**2']<o:p></o:p></p>
<p class="MsoNormal">R-value: 0.530<o:p></o:p></p>
<p class="MsoNormal">Estimated improvement of -0.450 A to d_min(FSCref=0.5): 6.628 A<o:p></o:p></p>
<p class="MsoNormal">Result: -0.450 A to d_min(FSCref=0.5): 6.628 A R-value: 0.530<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Wrote working map to /home/lawsond/phenix/ResolveCryoEM_1/map_denmod.ccp4<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">===============================================================================<o:p></o:p></p>
<p class="MsoNormal">SUMMARY AFTER CYCLE OF DENSITY-MODIFICATION<o:p></o:p></p>
<p class="MsoNormal">===============================================================================<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Overall best density modification Cycle 1 try 1<o:p></o:p></p>
<p class="MsoNormal">Estimated improvement: -0.450 A to d_min(FSCref=0.5): 6.628 A R-value: 0.530<o:p></o:p></p>
<p class="MsoNormal">Denmod resolution: 5.671 A<o:p></o:p></p>
<p class="MsoNormal">Database: 5.000 A<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Writing out final map files…<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">-------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Prof. David M. Lawson<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Department of Biological Chemistry,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">John Innes Centre,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Norwich,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">NR4 7UH, UK.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Tel: +44-(0)1603-450725<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Web: https://www.jic.ac.uk/people/david-lawson
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Email: david.lawson@jic.ac.uk<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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