<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Anne,<div><br></div><div>I'm sorry for the unclear labelling in that file. FP is 2FOFCWT and PHIM is PH2FOFCWT. I will try to make this more clear, and later, to use the right labels.</div><div><br></div><div>If you really want the original mtz file from phenix.refine with these coefficients, and the FOFCWT and PHFOFCWT coefficients, you can look in the TEMP0/ subdirectory, and find a file with a name like:</div><div><br></div><div>refine_map_coeffs_3.mtz</div><div><br></div><div>which will be the refinement map coefficients from refinement #3 . Look in the log file for something like:</div><div><br></div><div><div>New overall best saved:</div><div><br></div><div>Current overall_best model and map Thu Jan 15 07:14:48 2009</div><div>Working directory: /net/chevy/raid1/terwill/misc/test/AutoBuild_run_20_</div><div>Model (overall_best.pdb) from: Build_composite_refined_3.pdb</div><div><br></div><div>and that refined_3 goes with map_coeffs_3.</div><div><br></div><div>I hope that helps!</div><div>-Tom T</div><div><br></div></div><div><br></div><div><br><br><div><div>On Jan 15, 2009, at 3:20 AM, Anne M�lgaard wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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 lang="EN-US" link="blue" vlink="purple"><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; ">I am new to Phenix, so there might be an easy explanation for this problem, though I have not been able to find a solution in the documentation. I am using phenix version 1.3b-rc4, intel-linux-2.6.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; ">I have solved a structure using phenix.automr, followed by phenix.autobuild (run from command line using "phenix.autobuild data=fromXDS_unique.mtz model=AutoMR_run_2_/MR.1.pdb seq_file=sequence.fas"). The program runs succesfully, and I get the output files I should expect. However, the overall_best_refine_map_coeffs.mtz does not contain the map coefficients 2FOFCWT PH2FOFCWT for the 2mFo-DFc map and FOFC and PHFOFC for the Fo-Fc difference map. mtzdmp gives me the following columns:<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "> 1 ASC 0 28 0 100.00 10.6 10.6 28.28 1.85 H H<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "> 2 NONE 0 35 0 100.00 13.3 13.3 28.28 1.85 H K<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "> 3 NONE 0 71 0 100.00 26.6 26.6 28.28 1.85 H L<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "> 4 NONE 1.0 1888.8 0 100.00 148.71 148.71 28.28 1.85 F FP<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "> 5 BOTH 1.0 1.0 0 100.00 1.00 1.00 28.28 1.85 Q SIGFP<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "> 6 NONE -180.0 180.0 0 100.00 2.08 90.23 28.28 1.85 P PHIM<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "> 7 BOTH 1.000 1.000 0 100.00 1.000 1.000 28.28 1.85 W FOMM<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "> 8 NONE .0 19.0 0 100.00 9.50 9.50 28.28 1.85 I FreeR_flag<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "> 9 BOTH .0 .0 0 100.00 .00 .00 28.28 1.85 F FC<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; ">What should I do to get these map coefficients?<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; ">Thanks for your help!<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; ">Best regards,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Courier New"><span style="font-size: 10pt; font-family: 'Courier New'; ">Anne<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-left: 0cm; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div></div>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org" style="color: blue; text-decoration: underline; ">phenixbb@phenix-online.org</a><br><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb" style="color: blue; text-decoration: underline; ">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br></div></span></blockquote></div><br></div></body></html>