From owner-chemistry@ccl.net Wed Jan 4 06:49:00 2017 From: "Utpal Sarkar utpalchemiitkgp]~[gmail.com" To: CCL Subject: CCL:G: Understading the nature of molecular orbital (non bonding or sigma) Message-Id: <-52579-170104064724-3912-VoP6GyFL90BNUTMsL2JyWQ%%server.ccl.net> X-Original-From: "Utpal Sarkar" Date: Wed, 4 Jan 2017 06:47:23 -0500 Sent to CCL by: "Utpal Sarkar" [utpalchemiitkgp(0)gmail.com] Dear Gaussian users, I am trying to identify the molecular orbital transition for a particular peak of UV visible spectrum from Gaussian output. My question is how can I recognize weather a particular orbital is non bonding n orbital or sigma orbital? In my case, I have found for a particular peak at 237.93 nm with oscillator strength f=0.1806 and the responsible transitions are 41 -> 44 0.32998 41 -> 46 0.16625 42 -> 45 -0.21871 42 -> 47 0.19689 42 -> 48 0.29232 42 -> 50 -0.22757 42 -> 52 -0.14040 43 -> 46 -0.12852 43 -> 49 0.27673 Now I want to identify weather orbital number 42 is sigma or nonbonding n orbital. The coefficients of orbital number 42 is given below : 41 42 43 44 45 O O O V V Eigenvalues -- -0.27285 -0.24084 -0.23213 -0.05116 -0.04261 1 1 C 1S 0.00000 -0.00420 0.00000 0.00001 -0.00829 2 2S 0.00000 -0.00653 0.00000 0.00002 -0.01337 3 2PX 0.00000 -0.02012 -0.00001 0.00001 0.00289 4 2PY -0.00001 -0.00168 0.00000 -0.00002 0.01821 5 2PZ -0.13793 0.00001 0.02323 0.08393 0.00016 6 3S -0.00001 0.01777 0.00001 -0.00006 0.04398 7 3PX 0.00000 -0.02621 0.00000 0.00002 -0.00073 8 3PY -0.00001 -0.00037 0.00000 -0.00002 0.02348 9 3PZ -0.21271 0.00002 0.03355 0.12668 0.00024 10 4S 0.00001 0.04010 0.00010 -0.00041 0.13704 11 4PX -0.00001 -0.03987 -0.00012 -0.00001 -0.00228 12 4PY -0.00003 0.00962 0.00003 0.00003 0.06605 13 4PZ -0.20444 0.00003 0.04608 0.20909 0.00040 14 5S 0.00115 -0.35581 0.00042 0.00562 -2.59840 15 5PX -0.00036 0.37640 -0.00053 0.00004 -0.46640 16 5PY -0.00011 0.03293 0.00005 -0.00263 1.81287 17 5PZ -0.00891 0.00007 -0.01617 0.11613 0.00054 18 6D 0 0.00000 0.00022 0.00000 0.00000 -0.00167 19 6D+1 -0.00349 0.00000 -0.01518 -0.01160 -0.00002 20 6D-1 0.00841 0.00000 -0.00111 0.00349 0.00001 21 6D+2 0.00000 -0.00233 0.00000 0.00000 0.00518 22 6D-2 0.00000 0.00204 0.00000 0.00000 0.00069 23 2 C 1S 0.00000 0.00418 0.00000 0.00002 -0.00937 24 2S 0.00000 0.00682 0.00000 0.00003 -0.01539 25 2PX 0.00001 0.02532 0.00000 0.00003 -0.01284 26 2PY -0.00001 -0.00688 0.00001 -0.00001 0.00125 27 2PZ -0.03567 0.00001 0.08391 0.01761 -0.00001 28 3S -0.00002 -0.01999 0.00000 -0.00010 0.05218 29 3PX 0.00002 0.04132 0.00001 0.00005 -0.02390 30 3PY -0.00001 -0.00767 0.00002 -0.00002 0.00704 31 3PZ -0.05659 0.00002 0.13408 0.02588 -0.00002 32 4S -0.00002 -0.03998 -0.00006 -0.00023 0.17293 33 4PX -0.00002 0.05482 -0.00005 0.00033 -0.09711 34 4PY 0.00000 -0.07317 -0.00016 0.00003 -0.07289 35 4PZ -0.03986 0.00001 0.12373 0.02282 -0.00003 36 5S -0.00032 -0.11569 -0.00081 -0.01228 6.78260 37 5PX -0.00042 0.05717 -0.00013 0.00494 -1.60116 38 5PY -0.00059 0.44119 -0.00063 -0.00072 -1.24950 39 5PZ -0.02588 -0.00006 0.04361 0.17297 -0.00036 40 6D 0 0.00000 0.00018 0.00000 0.00001 -0.00208 41 6D+1 -0.02147 0.00000 0.00844 0.01814 0.00003 42 6D-1 -0.00727 0.00000 -0.01096 0.00789 0.00002 43 6D+2 -0.00001 0.00459 0.00000 -0.00001 0.00141 44 6D-2 0.00000 0.00783 0.00000 0.00000 0.00323 45 3 C 1S 0.00000 -0.00250 0.00001 0.00000 -0.00307 46 2S -0.00001 -0.00394 0.00001 0.00001 -0.00527 47 2PX 0.00000 -0.02120 0.00002 0.00000 -0.00284 48 2PY 0.00001 -0.00889 -0.00001 0.00001 -0.00383 49 2PZ 0.04067 0.00002 0.07965 -0.05872 -0.00012 50 3S 0.00002 0.00920 -0.00002 -0.00003 0.02598 51 3PX -0.00001 -0.03375 0.00006 0.00000 -0.00496 52 3PY 0.00002 -0.01359 -0.00002 0.00002 -0.00541 53 3PZ 0.06382 0.00003 0.12680 -0.09881 -0.00020 54 4S 0.00020 0.01844 -0.00050 0.00003 -0.00626 55 4PX 0.00001 -0.10072 0.00008 -0.00023 0.03817 56 4PY -0.00005 -0.02876 -0.00003 0.00013 -0.11338 57 4PZ 0.06310 0.00004 0.13146 -0.10786 -0.00029 58 5S -0.00091 1.35401 -0.00060 -0.00343 1.95224 59 5PX 0.00011 -0.07907 -0.00052 -0.01066 4.45406 60 5PY -0.00021 0.25218 -0.00015 0.00362 -2.43405 61 5PZ 0.02754 0.00003 -0.00041 -0.30749 -0.00068 62 6D 0 0.00000 -0.00126 0.00000 0.00001 -0.00313 63 6D+1 0.02091 0.00000 0.01506 0.02310 0.00003 64 6D-1 -0.00972 0.00000 0.00984 0.00010 -0.00001 65 6D+2 0.00001 0.00092 0.00000 0.00001 -0.00749 66 6D-2 0.00000 0.00700 -0.00001 0.00000 -0.00141 67 4 C 1S 0.00000 0.00209 0.00000 0.00002 -0.01205 68 2S 0.00000 0.00332 -0.00001 0.00003 -0.01967 69 2PX 0.00000 0.01269 -0.00001 0.00001 -0.00401 70 2PY -0.00001 -0.00223 0.00001 0.00002 -0.02944 71 2PZ 0.13807 -0.00001 0.03273 0.09279 0.00016 72 3S -0.00001 -0.01048 0.00002 -0.00011 0.07052 73 3PX 0.00001 0.01699 -0.00002 0.00003 -0.00983 74 3PY -0.00002 -0.00209 0.00001 0.00002 -0.03833 75 3PZ 0.21444 -0.00001 0.04852 0.14133 0.00025 76 4S -0.00007 0.03587 0.00010 0.00012 0.02042 77 4PX 0.00005 0.01075 -0.00004 -0.00013 0.06745 78 4PY -0.00002 0.03088 0.00003 0.00014 -0.08716 79 4PZ 0.19966 -0.00001 0.05466 0.21749 0.00040 80 5S 0.00048 0.24000 0.00046 0.01370 -6.29902 81 5PX 0.00014 0.15294 0.00022 -0.00038 0.95984 82 5PY 0.00016 0.03045 -0.00005 0.00288 -2.02375 83 5PZ 0.02481 -0.00001 0.02389 0.30485 0.00041 84 6D 0 0.00000 -0.00014 0.00000 0.00000 -0.00113 85 6D+1 0.00307 0.00000 -0.01335 0.00485 0.00001 86 6D-1 0.00725 0.00000 0.00326 -0.00480 -0.00001 87 6D+2 0.00000 0.00252 0.00000 0.00000 0.00556 88 6D-2 0.00000 0.00085 0.00000 0.00000 -0.00282 89 5 C 1S 0.00000 -0.00128 0.00000 0.00000 -0.00810 90 2S 0.00000 -0.00204 0.00000 0.00001 -0.01317 91 2PX 0.00000 -0.00832 0.00001 -0.00002 0.02313 92 2PY 0.00000 -0.00240 0.00001 0.00000 -0.01084 93 2PZ 0.06902 -0.00002 -0.06649 -0.02215 -0.00004 94 3S -0.00001 0.00606 0.00000 -0.00002 0.04591 95 3PX 0.00000 -0.01115 0.00001 -0.00003 0.03168 96 3PY -0.00001 -0.00283 0.00001 0.00001 -0.01523 97 3PZ 0.10653 -0.00003 -0.10344 -0.03512 -0.00007 98 4S 0.00000 -0.01037 -0.00002 -0.00007 0.04618 99 4PX 0.00000 0.00126 0.00003 -0.00004 0.05818 100 4PY 0.00002 -0.00822 0.00000 -0.00002 -0.01083 101 4PZ 0.09937 -0.00003 -0.10252 -0.04632 -0.00010 102 5S -0.00035 -0.82701 0.00051 0.00144 0.52163 103 5PX 0.00017 0.10769 0.00005 -0.00063 0.66730 104 5PY 0.00005 -0.08692 0.00039 0.00162 -0.24277 105 5PZ 0.01608 0.00001 -0.03265 -0.08881 -0.00014 106 6D 0 0.00000 -0.00007 0.00000 0.00000 -0.00241 107 6D+1 -0.01473 0.00000 -0.00471 -0.01392 -0.00002 108 6D-1 -0.01513 0.00000 -0.00919 -0.01697 -0.00003 109 6D+2 0.00000 -0.00040 0.00000 0.00000 -0.00226 110 6D-2 0.00000 0.00182 0.00000 -0.00001 0.00809 111 6 C 1S 0.00000 0.00206 0.00000 0.00001 -0.00756 112 2S 0.00000 0.00328 0.00000 0.00001 -0.01224 113 2PX 0.00000 0.01042 0.00000 -0.00002 0.01938 114 2PY 0.00000 -0.00458 0.00000 0.00000 0.00515 115 2PZ -0.08000 -0.00001 -0.07284 -0.07944 -0.00013 116 3S 0.00000 -0.00969 -0.00001 -0.00003 0.04258 117 3PX 0.00000 0.01483 0.00000 -0.00003 0.02922 118 3PY 0.00001 -0.00640 0.00000 0.00001 0.00699 119 3PZ -0.12304 -0.00001 -0.11316 -0.12197 -0.00020 120 4S -0.00002 0.00460 0.00005 0.00008 0.05411 121 4PX 0.00001 0.00771 -0.00002 -0.00004 0.01724 122 4PY 0.00001 -0.00624 0.00003 0.00001 0.01256 123 4PZ -0.11495 -0.00001 -0.11594 -0.18994 -0.00033 124 5S -0.00009 0.16872 -0.00011 -0.00994 4.64091 125 5PX 0.00005 -0.06078 -0.00020 0.00194 -0.77473 126 5PY 0.00014 -0.25334 0.00036 0.00074 0.22739 127 5PZ -0.02468 -0.00005 -0.01066 -0.15953 -0.00042 128 6D 0 0.00000 0.00004 0.00000 0.00000 -0.00184 129 6D+1 0.01185 0.00000 -0.00198 -0.01019 -0.00002 130 6D-1 -0.01584 0.00000 0.00844 0.00961 0.00002 131 6D+2 0.00000 0.00150 0.00000 0.00000 -0.00427 132 6D-2 0.00000 0.00180 0.00000 0.00001 -0.00663 133 7 H 1S 0.00000 0.00276 0.00000 -0.00001 -0.00016 134 2S 0.00000 0.00033 -0.00002 -0.00001 -0.01090 135 3S 0.00001 -0.00344 -0.00001 0.00012 -0.13711 136 4S 0.00003 -0.06299 -0.00001 0.00187 -1.54608 137 5PX 0.00000 -0.00055 0.00000 0.00000 -0.00001 138 5PY 0.00000 0.00060 0.00000 0.00001 -0.00575 139 5PZ -0.01251 0.00000 0.00163 0.00961 0.00002 140 8 H 1S 0.00001 -0.00311 0.00000 0.00000 0.00078 141 2S 0.00002 0.00008 -0.00001 -0.00001 -0.00098 142 3S 0.00002 0.01171 -0.00001 0.00021 -0.15692 143 4S 0.00005 -0.02814 -0.00004 0.00174 -1.97399 144 5PX 0.00000 0.00049 0.00000 0.00000 0.00052 145 5PY 0.00000 0.00042 0.00000 -0.00001 0.01084 146 5PZ 0.01269 0.00000 0.00269 0.01163 0.00002 147 9 H 1S 0.00000 -0.00582 0.00000 0.00000 -0.00246 148 2S 0.00001 -0.01106 0.00000 0.00000 -0.01231 149 3S 0.00000 -0.01276 0.00001 0.00008 -0.10144 150 4S -0.00004 -0.03749 0.00007 0.00121 -1.35734 151 5PX 0.00000 -0.00017 0.00000 0.00000 -0.00629 152 5PY 0.00000 -0.00055 0.00000 0.00000 0.00507 153 5PZ 0.00639 0.00000 -0.00659 -0.00303 -0.00001 154 10 H 1S 0.00000 0.00742 0.00000 0.00000 -0.00369 155 2S 0.00000 0.01212 0.00000 0.00000 -0.01105 156 3S -0.00001 0.01434 0.00002 0.00005 -0.06846 157 4S -0.00004 0.05825 0.00006 0.00002 -0.75096 158 5PX 0.00000 0.00023 0.00000 0.00000 -0.00645 159 5PY 0.00000 -0.00057 0.00000 0.00000 -0.00321 160 5PZ -0.00740 0.00000 -0.00708 -0.01018 -0.00002 161 11 N 1S 0.00000 0.01372 -0.00001 0.00003 -0.00782 162 2S -0.00001 0.02167 -0.00001 0.00006 -0.01277 163 2PX -0.00002 0.04387 -0.00004 0.00005 -0.01666 164 2PY 0.00003 -0.02001 0.00003 0.00001 -0.01927 165 2PZ -0.09681 0.00000 -0.09374 -0.07140 -0.00005 166 3S 0.00002 -0.05881 0.00002 -0.00018 0.04236 167 3PX -0.00002 0.06205 -0.00006 0.00007 -0.02270 168 3PY 0.00005 -0.02060 0.00004 0.00001 -0.03001 169 3PZ -0.14942 0.00001 -0.14256 -0.10704 -0.00008 170 4S 0.00002 -0.25348 0.00023 -0.00037 0.09649 171 4PX -0.00010 0.07780 0.00005 0.00005 -0.05391 172 4PY 0.00002 -0.07692 0.00024 -0.00010 0.00907 173 4PZ -0.16396 -0.00005 -0.17391 -0.16705 -0.00011 174 5S 0.00008 -0.31318 0.00020 -0.00140 0.89693 175 5PX -0.00024 -0.09505 0.00045 -0.00043 -0.21030 176 5PY -0.00024 -0.15548 0.00046 0.00029 -0.33094 177 5PZ -0.05292 0.00003 -0.05002 -0.17772 -0.00018 178 6D 0 0.00000 -0.00185 0.00000 0.00002 -0.00149 179 6D+1 0.00364 0.00000 0.00520 -0.02009 -0.00003 180 6D-1 -0.00039 0.00000 -0.00057 0.01129 0.00001 181 6D+2 0.00000 0.00150 0.00000 -0.00001 0.00611 182 6D-2 0.00000 -0.00183 0.00000 0.00000 0.00022 183 12 S 1S 0.00000 0.00290 0.00000 -0.00001 0.00163 184 2S 0.00000 0.00837 0.00000 -0.00003 0.00464 185 3S 0.00000 -0.01879 -0.00001 0.00006 -0.00998 186 4S 0.00000 -0.03107 -0.00001 0.00011 -0.01976 187 5S 0.00000 0.06171 0.00001 -0.00029 0.05265 188 6S -0.00006 0.14997 0.00031 0.00004 -0.02952 189 7S -0.00086 -0.63601 0.00275 0.00698 -2.70572 190 7PX 0.00011 0.08675 -0.00009 0.00205 -0.38791 191 7PY 0.00022 0.16721 -0.00061 -0.00068 0.46445 192 7PZ -0.02854 -0.00013 0.04463 -0.19770 -0.00015 193 8PX 0.00000 0.01606 0.00000 -0.00004 0.01283 194 8PY -0.00003 0.01951 0.00002 -0.00003 0.00473 195 8PZ -0.04816 0.00002 0.04326 0.02805 0.00002 196 9PX 0.00000 0.03105 0.00000 -0.00008 0.02428 197 9PY -0.00006 0.03729 0.00004 -0.00006 0.00882 198 9PZ -0.09209 0.00003 0.08258 0.05304 0.00004 199 10PX 0.00000 -0.04744 -0.00001 0.00011 -0.03405 200 10PY 0.00008 -0.05379 -0.00005 0.00009 -0.01131 201 10PZ 0.13230 -0.00004 -0.11935 -0.07694 -0.00007 202 11PX 0.00001 -0.08915 -0.00001 0.00029 -0.09302 203 11PY 0.00018 -0.12713 -0.00019 0.00022 -0.04127 204 11PZ 0.28539 -0.00008 -0.26406 -0.19142 -0.00016 205 12PX 0.00005 -0.03524 0.00007 0.00081 -0.22530 206 12PY 0.00014 -0.09592 -0.00016 0.00003 0.02799 207 12PZ 0.15826 -0.00003 -0.19006 -0.20245 -0.00022 208 13D 0 0.00001 0.00601 -0.00001 0.00005 -0.00229 209 13D+1 -0.00454 -0.00001 0.00983 -0.02539 -0.00003 210 13D-1 -0.00987 -0.00001 0.00459 -0.04352 -0.00003 211 13D+2 0.00000 -0.01900 -0.00002 -0.00003 0.01677 212 13D-2 0.00000 0.00397 0.00000 0.00003 -0.01970 213 13 C 1S 0.00000 -0.00054 0.00001 -0.00007 0.00707 214 2S 0.00000 -0.00087 0.00001 -0.00011 0.01133 215 2PX 0.00000 0.00412 0.00000 0.00002 -0.01209 216 2PY 0.00000 0.00413 0.00000 0.00006 -0.01879 217 2PZ 0.00044 0.00001 0.00137 0.19642 0.0002 218 3S 0.00000 -0.00105 -0.00002 0.00032 -0.02794 219 3PX 0.00000 0.00728 0.00001 0.00004 -0.02614 220 3PY 0.00000 0.01138 0.00001 0.00009 -0.03399 221 3PZ 0.00049 0.00002 0.00146 0.30948 0.00035 222 4S -0.00002 0.11622 -0.00015 0.00089 -0.17612 223 4PX 0.00009 0.10208 -0.00035 0.00019 -0.04885 224 4PY 0.00008 -0.15266 -0.00010 0.00015 -0.00317 225 4PZ 0.02778 0.00000 0.02512 0.47540 0.00056 226 5S -0.00002 0.24610 -0.00057 -0.00686 2.55118 227 5PX 0.00063 0.06008 -0.00196 -0.00210 0.82602 228 5PY 0.00056 0.32064 -0.00117 0.00218 -0.06420 229 5PZ 0.00365 -0.00003 0.00989 0.49364 -0.00012 230 6D 0 0.00000 0.00053 0.00000 0.00002 -0.00347 231 6D+1 -0.00533 -0.00001 -0.03539 0.00094 0.00000 232 6D-1 0.01987 0.00000 -0.00369 0.00682 0.00000 233 6D+2 0.00000 -0.01008 0.00002 0.00001 -0.00922 234 6D-2 0.00001 0.04164 0.00000 0.00000 0.00012 235 14 S 1S 0.00000 -0.00023 0.00000 -0.00001 0.00057 236 2S 0.00000 -0.00066 0.00000 -0.00002 0.00160 237 3S 0.00000 0.00144 0.00000 0.00004 -0.00315 238 4S 0.00000 0.00259 0.00000 0.00008 -0.00798 239 5S 0.00000 -0.00662 0.00001 -0.00018 0.02430 240 6S 0.00011 0.01941 -0.00027 0.00004 -0.03475 241 7S 0.00088 0.10246 -0.00234 0.00077 0.12869 242 7PX 0.00021 0.01705 -0.00053 0.00011 0.07181 243 7PY 0.00000 0.04548 -0.00001 -0.00031 0.05435 244 7PZ 0.00797 0.00000 -0.04975 -0.23449 -0.00012 245 8PX 0.00000 -0.01267 0.00005 0.00001 0.00038 246 8PY 0.00002 0.09670 -0.00002 0.00000 0.00285 247 8PZ -0.00531 -0.00001 -0.07103 0.04261 0.00005 248 9PX 0.00001 -0.02407 0.00009 0.00003 0.00077 249 9PY 0.00003 0.18538 -0.00003 0.00000 0.00564 250 9PZ -0.01020 -0.00003 -0.13601 0.08045 0.00009 251 10PX -0.00001 0.03338 -0.00012 -0.00004 -0.00168 252 10PY -0.00004 -0.26602 0.00004 0.00001 -0.00954 253 10PZ 0.01444 0.00004 0.19208 -0.11091 -0.00012 254 11PX 0.00002 0.07699 -0.00034 -0.00006 0.00332 255 11PY -0.00009 -0.53528 0.00009 0.00002 -0.01279 256 11PZ 0.02904 0.00009 0.41149 -0.29074 -0.00033 257 12PX 0.00003 0.06051 -0.00024 0.00035 -0.11187 258 12PY -0.00008 -0.36514 0.00009 -0.00007 -0.02518 259 12PZ 0.00517 0.00006 0.25799 -0.27088 -0.00028 260 13D 0 0.00000 0.00005 0.00002 0.00006 -0.00304 261 13D+1 0.00124 0.00001 0.01518 0.05558 0.00007 262 13D-1 0.00295 -0.00001 0.00167 0.00834 0.00001 263 13D+2 0.00000 0.00432 -0.00001 -0.00002 0.00215 264 13D-2 -0.00001 -0.02106 0.00000 0.00000 -0.00360 265 15 H 1S 0.00000 0.00080 0.00001 0.00002 -0.00804 266 2S -0.00002 0.01162 0.00008 0.00001 -0.00684 267 3S -0.00015 -0.02440 0.00023 0.00024 -0.29261 268 4S 0.00000 0.10929 0.00001 0.00126 -0.61549 269 5PX 0.00000 -0.00083 0.00000 0.00000 -0.00002 270 5PY 0.00000 0.00011 0.00001 -0.00002 0.01104 271 5PZ -0.00915 0.00000 -0.00861 -0.00943 0.00000 Any type of help is highly appreciated. regards utpal From owner-chemistry@ccl.net Wed Jan 4 12:29:01 2017 From: "John McKelvey jmmckel*gmail.com" To: CCL Subject: CCL: Protein structures Message-Id: <-52580-170104121650-28382-ehlMfjciNOBb+8gEUhHMDA:server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=f403045ea48eec7163054547f2b8 Date: Wed, 4 Jan 2017 11:16:43 -0600 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel././.gmail.com] --f403045ea48eec7163054547f2b8 Content-Type: text/plain; charset=UTF-8 Folks, I realize that over time development of technology may have an impact on reliability or accuracy of protein XRAY structures. How does one determine accuracy or reliability of such structures? Ignoring hardware and software demands for the moment is it preferable/practical/wise to optimize such a structure? Many thanks! John -- John McKelvey 545 Legacy Pointe Dr O'Fallon, MO 63376 636-294-5203 jmmckel/./gmail.com --f403045ea48eec7163054547f2b8 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Folks,

I realize that over tim= e development of technology may have an impact on reliability or accuracy o= f protein XRAY structures.=C2=A0 How does one determine accuracy or reliabi= lity of such structures?=C2=A0 Ignoring hardware and software demands for t= he moment is it preferable/practical/wise to optimize such a structure?
=
Many thanks!

John

--
John McKelvey
545 Legac= y Pointe Dr
O'Fallon, MO 63376
636-294-5203
jmmckel/./gmail.com
--f403045ea48eec7163054547f2b8-- From owner-chemistry@ccl.net Wed Jan 4 16:46:00 2017 From: "Jim Kress jimkress35.]~[.gmail.com" To: CCL Subject: CCL: Protein structures Message-Id: <-52581-170104164221-18500-+OoiMN6fSgbzGqkl1RuueA]~[server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_01A2_01D266A9.7AC67BA0" Date: Wed, 4 Jan 2017 16:42:03 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35]-[gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_01A2_01D266A9.7AC67BA0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable > Ignoring hardware and software demands for the moment is it = preferable/practical/wise to optimize such a structure? =20 It depends on whether it is intrinsically disordered or not. It also = depends on whether you want an in vivo representation or if you think = the in-vacuo representation is representative of the actual structure in = vivo. =20 Jim =20 > From: owner-chemistry+jimkress35=3D=3Dgmail.com!A!ccl.net = [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com!A!ccl.net] On Behalf Of = John McKelvey jmmckel*gmail.com Sent: Wednesday, January 04, 2017 12:17 PM To: Kress, Jim Subject: CCL: Protein structures =20 Folks, I realize that over time development of technology may have an impact on = reliability or accuracy of protein XRAY structures. How does one = determine accuracy or reliability of such structures? Ignoring hardware = and software demands for the moment is it preferable/practical/wise to = optimize such a structure? Many thanks! John --=20 John McKelvey 545 Legacy Pointe Dr O'Fallon, MO 63376 636-294-5203 jmmckel{:}gmail.com =20 ------=_NextPart_000_01A2_01D266A9.7AC67BA0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

> = Ignoring hardware and software demands for the moment is it = preferable/practical/wise to optimize such a = structure?

 

It depends = on whether it is intrinsically disordered or not.=C2=A0 It also depends = on whether you want an in vivo representation or if you think the = in-vacuo representation is representative of the actual structure in = vivo.

 

Jim

 

From:<= /b> = owner-chemistry+jimkress35=3D=3Dgmail.com!A!ccl.net = [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com!A!ccl.net] On Behalf = Of John McKelvey jmmckel*gmail.com
Sent: Wednesday, = January 04, 2017 12:17 PM
To: Kress, Jim = <jimkress35!A!gmail.com>
Subject: CCL: Protein = structures

 

Folks,

I realize that over = time development of technology may have an impact on reliability or = accuracy of protein XRAY structures.  How does one determine = accuracy or reliability of such structures?  Ignoring hardware and = software demands for the moment is it preferable/practical/wise to = optimize such a structure?

Many thanks!

John


--

John McKelvey
545 Legacy Pointe = Dr

O'Fallon, MO = 63376
636-294-5203
jmmckel{:}gmail.com

------=_NextPart_000_01A2_01D266A9.7AC67BA0-- From owner-chemistry@ccl.net Wed Jan 4 21:16:00 2017 From: "Gregory L Warren greg#,#eyesopen.com" To: CCL Subject: CCL: Protein structures Message-Id: <-52582-170104185826-22000-BDDhWlMwPqZH5LkqbGhcTw^^^server.ccl.net> X-Original-From: "Gregory L Warren" Date: Wed, 4 Jan 2017 18:58:24 -0500 Sent to CCL by: "Gregory L Warren" [greg[a]eyesopen.com] Dear John, Unfortunately X-ray (and neutron) diffraction structures are a model of experimental data and as such will always have reliability and accuracy issues embedded in the model. What is not clear to me is what you mean by reliability or accuracy and if by accuracy do you mean precision? If by reliability improvements you mean a reduction in the number of bond, angle, torsion and clash violations then yes improvements in software have resulted in the models having fewer of these problems than structures published 10 to 30 years ago. Improvements in X-ray sources and detectors have lowered the amount of noise present in the data so theoretically structures should be more precise now than the historically. For true accuracy, i.e. how well does the model represent the data, there has always been a problem with generating single model for what is time and conformationally (both in the lattice and thermally) averaged data. This practice, by in large, has not changed. So how can we assess whether a model is reliably, precise, and seems to be a reasonable model for the data? There are publications that look at this and out of laziness I will only point you to one I authored (GL Warren et al., Drug Discovery Today, 17, 1270, (2012)). I will summarize below. For reliability: Look at or regenerate the wwPDB validation report http://wwpdb.org/validation/2016/XrayValidationReportHelp Parts of the report are shown on the RCSB web site for each structure. These values help to let you know how the model compares to other models in the database and is a good indicator of reliability. I find the global validation metric picture very helpful. For precision: Use Density Precision Index (DPI) which was reported in the EDS (electron density server) but that is being retired in 2017. Sometimes the information is in the pdb header and you can calculate the value yourself from information in the header. Do not use resolution as it is meaningless for understanding the quality of the data and the quality of the model. For accuracy: Look at the R-factor and Rfree (or CC1/2). This is a good indicator as to how well the model fits the data. A good rule of thumb is that the R-factor (or R-free) should not be much more than 0.1 times the resolution, i.e. 2.5 A structure R-free 0.25. Unfortunately R-free cannot be used to sort models from different data sets. Last, what do you mean by optimize? I routinely re-refine structures particularly if I have a number of structures I want to look at for method development or validation. This is not done to improve the structures but to remove any variability present because structures are determined using different refinement methods and I want to remove the method variance from my data. I would recommend re-refining a structure after adding hydrogen. For me this is a cheap and easy way to optimize the structure after hydrogen addition while ensuring that the optimization is restrained by the data rather than an artificial restraint that may or may not be relevant for that structure. Very last. If the structure contains a ligand I care about then I almost always re-refine the structure and refit the ligand. This is particularly true if the structure was determined in an academic laboratory versus from a pharmaceutical companys structural biology group. Historically small molecule conformations have been very poor if you are concerned with calculating energy values and I see little evidence that structures currently being deposited have improved dramatically. Regards, Greg ---- Gregory Warren, PhD Senior Applications Scientist OpenEye Scientific Software, Inc 9 Bisbee Court, Suite D Santa Fe, NM 87508 (505) 240-6956 greg^^eyesopen.com > From: owner-chemistry+greg==eyesopen.com^^ccl.net [mailto:owner- chemistry+greg==eyesopen.com^^ccl.net] On Behalf Of John McKelvey jmmckel*gmail.com Sent: Wednesday, January 04, 2017 10:17 AM To: Greg Warren Subject: CCL: Protein structures Folks, I realize that over time development of technology may have an impact on reliability or accuracy of protein XRAY structures. How does one determine accuracy or reliability of such structures? Ignoring hardware and software demands for the moment is it preferable/practical/wise to optimize such a structure? Many thanks! John -- John McKelvey 545 Legacy Pointe Dr O'Fallon, MO 63376 636-294-5203 jmmckel{:}gmail.com From owner-chemistry@ccl.net Wed Jan 4 22:37:00 2017 From: "Lars Goerigk lars.goerigk#unimelb.edu.au" To: CCL Subject: CCL: Protein structures Message-Id: <-52583-170104205328-26276-HEchTXI1ow5fq8yfLINZtQ{=}server.ccl.net> X-Original-From: Lars Goerigk Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_CE24172FE0564E6A85FC62F2AE46F1C3unimelbeduau_" Date: Thu, 5 Jan 2017 01:53:08 +0000 MIME-Version: 1.0 Sent to CCL by: Lars Goerigk [lars.goerigk+*+unimelb.edu.au] --_000_CE24172FE0564E6A85FC62F2AE46F1C3unimelbeduau_ Content-Type: text/plain; charset=WINDOWS-1252 Content-Transfer-Encoding: quoted-printable Hi John, not sure if this is helpful as a starting point, but an analysis of common = methods for geometry optimisations in periodic boundary conditions, incl. a= comparison with a crystal structure and free R-factors, has been published= in J. Phys Chem B 2014, 118, 14612-14626. Therein you can also find a literatu= re review and a summary of the work by Ryde and Thiel in the area of quantu= m refinement of protein X-ray structures with QM/MM. Best wishes, Lars Dr Lars Goerigk | Lecturer & ARC DECRA Fellow School of Chemistry | The University of Melbourne Victoria 3010 | Australia Website: goerigk.chemistry.unimelb.edu.au Follow me on Twitter: https://twitter.com/lgoer_compchem On 5 Jan 2017, at 8:42 am, Jim Kress jimkress35. : .gmail.com > wrote: > Ignoring hardware and software demands for the moment is it preferable/pr= actical/wise to optimize such a structure? It depends on whether it is intrinsically disordered or not. It also depen= ds on whether you want an in vivo representation or if you think the in-vac= uo representation is representative of the actual structure in vivo. Jim > From: owner-chemistry+jimkress35=3D=3Dgmail.com]![ccl.ne= t [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com]![ccl.net] On Behalf Of John McKelvey jmmckel= *gmail.com Sent: Wednesday, January 04, 2017 12:17 PM To: Kress, Jim > Subject: CCL: Protein structures Folks, I realize that over time development of technology may have an impact on re= liability or accuracy of protein XRAY structures. How does one determine a= ccuracy or reliability of such structures? Ignoring hardware and software = demands for the moment is it preferable/practical/wise to optimize such a s= tructure? Many thanks! John -- John McKelvey 545 Legacy Pointe Dr O'Fallon, MO 63376 636-294-5203 jmmckel{:}gmail.com --_000_CE24172FE0564E6A85FC62F2AE46F1C3unimelbeduau_ Content-Type: text/html; charset=WINDOWS-1252 Content-ID: <765E61115CA27844A4F369F9B56718A4 : ausprd01.prod.outlook.com> Content-Transfer-Encoding: quoted-printable Hi John,

not sure if this is helpful as a starting point, but an analysis of co= mmon methods for geometry optimisations in periodic boundary conditions, in= cl. a comparison with a crystal structure and free R-factors, has been publ= ished in

J. Phys Chem B 2014, 118, 14612-14626. Therein you can a= lso find a literature review and a summary of the work by Ryde and Thiel in= the area of quantum refinement of  protein X-ray structures with QM/M= M.

Best wishes,

Lars


Dr Lars Goerigk | Lecturer & ARC DECRA Fellow
School of Chemistry | The University of Melbourne
Victoria 3010 | Australia
Follow me on Twitter: https://twitter.com/lgoer_compche= m

On 5 Jan 2017, at 8:42 am, Jim Kress jimkress35. : .gmail.com <owner= -chemistry : ccl.net> wrote:

> Ign= oring hardware and software demands for the moment is it preferable/practic= al/wise to optimize such a structure?
 
It depen= ds on whether it is intrinsically disordered or not.  It also depends = on whether you want an in vivo representation or if you think the in-vacuo = representation is representative of the actual structure in vivo.
 
Jim=
 
From:=  owner-chemistry+jimkr= ess35=3D=3Dgmail.com]![ccl.net [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com]![ccl.net]&n= bsp;On Behalf Of John McKel= vey jmmckel*gmail.com
Sent: Wednesday, J= anuary 04, 2017 12:17 PM
To: Kress, Jim <= ;jimkress35]![gmail.com>
Subject: CCL: Prot= ein structures
 

Folks,

I realize that over time development of technology may have an impact on re= liability or accuracy of protein XRAY structures.  How does one determ= ine accuracy or reliability of such structures?  Ignoring hardware and= software demands for the moment is it preferable/practical/wise to optimize such a structure?

Many thanks!

John

--
John McKelvey
545 Legacy Pointe Dr
O'Fallon, MO 63376
636-294-5203
jmmckel{:}gmail.com

--_000_CE24172FE0564E6A85FC62F2AE46F1C3unimelbeduau_--