<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ken,<div><br></div><div>I am guessing that all these atoms somehow fall in one omit region...so in that omit run there is a PDB file with all zero occupancies. Is that possible? If so...then a solution would be to make very small omit regions.</div><div><br></div><div>However it may be instead that you want to be using a different PDB file to start with. Your input PDB file for the omit run usually will have your entire structure in it. If you want to mark the region to omit, you would separately supply a PDB file with the atoms marking the region to omit.</div><div><br></div><div>I hope that helps!</div><div>All the best,</div><div>Tom T</div><div><br><div><div>On Aug 26, 2011, at 2:42 PM, Kenneth A. Satyshur wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>I am running omit map on pdb file and I get <br>Failed to carry out AutoBuild_build_cycle:<br><br>Initial phenix refinement of AutoBuild_run_22_/edited_pdb.pdb with exptl_fobs_phases_freeR_flags.mtz failed...quitting...<br>/usr/keck/u1/PriA/APS_Aug2011/phasing/AutoBuild_run_22_/LAST.LOG may have additional information...<br>All occupancies in input PDB file are zero.<br><br><br>yet<br><br>CRYST1 85.433 85.433 111.682 90.00 90.00 120.00 P 32 <br>SCALE1 0.011705 0.006758 0.000000 0.00000 <br>SCALE2 0.000000 0.013516 0.000000 0.00000 <br>SCALE3 0.000000 0.000000 0.008954 0.00000 <br>ATOM 931 N ALA N 308 4.340 -30.086 -9.129 1.00 39.02 N<br>ATOM 932 CA ALA N 308 4.553 -29.451 -10.458 1.00 38.92 C<br>ATOM 933 CB ALA N 308 3.225 -29.326 -11.198 1.00 38.66 C<br>ATOM 934 C ALA N 308 5.202 -28.079 -10.295 1.00 37.85 C<br>ATOM 935 O ALA N 308 5.278 -27.555 -9.185 1.00 38.80 O<br>ATOM 936 N ALA N 309 5.633 -27.505 -11.414 1.00 36.99 N<br>ATOM 937 CA ALA N 309 6.216 -26.142 -11.498 1.00 37.18 C<br>ATOM 938 CB ALA N 309 5.194 -25.019 -11.222 1.00 36.42 C<br>ATOM 939 C ALA N 309 7.457 -25.985 -10.646 1.00 34.05 C<br>ATOM 940 O ALA N 309 7.404 -26.148 -9.436 1.00 31.65 O<br>ATOM 941 N ALA N 310 8.570 -25.673 -11.311 1.00 34.03 N<br>ATOM 942 CA ALA N 310 9.883 -25.614 -10.696 1.00 34.33 C<br>ATOM 943 CB ALA N 310 10.332 -24.166 -10.573 1.00 31.89 C<br>ATOM 944 C ALA N 310 9.895 -26.350 -9.337 1.00 36.59 C<br>ATOM 945 O ALA N 310 10.250 -25.773 -8.304 1.00 40.46 O<br>ATOM 946 N ALA N 311 9.479 -27.623 -9.364 1.00 36.20 N<br>ATOM 947 CA ALA N 311 9.321 -28.471 -8.174 1.00 33.93 C<br>ATOM 948 CB ALA N 311 8.446 -29.664 -8.503 1.00 34.46 C<br>ATOM 949 C ALA N 311 10.659 -28.948 -7.641 1.00 32.37 C<br>ATOM 950 O ALA N 311 10.943 -30.156 -7.619 1.00 31.59 O<br>ATOM 951 N ALA N 312 11.479 -27.982 -7.229 1.00 30.93 N<br>ATOM 952 CA ALA N 312 12.821 -28.234 -6.694 1.00 30.94 C<br>ATOM 953 CB ALA N 312 12.740 -28.872 -5.308 1.00 30.60 C<br>ATOM 954 C ALA N 312 13.680 -29.080 -7.647 1.00 30.22 C<br>ATOM 955 O ALA N 312 13.405 -29.148 -8.853 1.00 32.14 O<br>ATOM 956 N PRO N 313 14.739 -29.702 -7.116 1.00 28.06 N<br>ATOM 957 CA PRO N 313 15.519 -30.706 -7.852 1.00 27.14 C<br>ATOM 958 CB PRO N 313 16.820 -30.771 -7.044 1.00 27.81 C<br>ATOM 959 CG PRO N 313 16.871 -29.482 -6.264 1.00 28.11 C<br>they don't look zero to me.<br><br>anyone get this error?<br><br><br>--<br>Kenneth A. Satyshur, M.S.,Ph.D.<br>Associate Scientist<br>University of Wisconsin<br>Madison, Wisconsin 53706<br>608-215-5207<br><span><satyshur.vcf></span>_______________________________________________<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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