From owner-chemistry@ccl.net Wed Jan 4 06:49:00 2017
From: "Utpal Sarkar utpalchemiitkgp]~[gmail.com" <owner-chemistry%%server.ccl.net>
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" <utpalchemiitkgp+*+gmail.com>
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" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: Protein structures
Message-Id: <-52580-170104121650-28382-ehlMfjciNOBb+8gEUhHMDA:server.ccl.net>
X-Original-From: John McKelvey <jmmckel#,#gmail.com>
Content-Type: multipart/alternative; boundary=f403045ea48eec7163054547f2b8
Date: Wed, 4 Jan 2017 11:16:43 -0600
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Sent to CCL by: John McKelvey [jmmckel././.gmail.com]
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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
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<div dir=3D"ltr"><div><div><div>Folks,<br><br></div>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?<br>=
<br></div>Many thanks!<br><br></div>John<br clear=3D"all"><div><div><div><d=
iv><br>-- <br><div class=3D"gmail_signature" data-smartmail=3D"gmail_signat=
ure"><div dir=3D"ltr"><div><div dir=3D"ltr"><div>John McKelvey<br>545 Legac=
y Pointe Dr</div><div>O'Fallon, MO 63376<br>636-294-5203<br><a href=3D"=
mailto:jmmckel/./gmail.com" target=3D"_blank">jmmckel/./gmail.com</a></div></di=
v></div></div></div>
</div></div></div></div></div>
--f403045ea48eec7163054547f2b8--
From owner-chemistry@ccl.net Wed Jan 4 16:46:00 2017
From: "Jim Kress jimkress35.]~[.gmail.com" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: Protein structures
Message-Id: <-52581-170104164221-18500-+OoiMN6fSgbzGqkl1RuueA]~[server.ccl.net>
X-Original-From: "Jim Kress" <jimkress35,+,gmail.com>
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 <jimkress35!A!gmail.com>
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 <mailto:jmmckel%7b:%7dgmail.com>=20
------=_NextPart_000_01A2_01D266A9.7AC67BA0
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charset="UTF-8"
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xmlns:o=3D"urn:schemas-microsoft-com:office:office" =
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xmlns:m=3D"http://schemas.microsoft.com/office/2004/12/omml" =
xmlns=3D"http://www.w3.org/TR/REC-html40"><head><meta =
http-equiv=3DContent-Type content=3D"text/html; charset=3Dutf-8"><meta =
name=3DGenerator content=3D"Microsoft Word 15 (filtered =
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<o:idmap v:ext=3D"edit" data=3D"1" />
</o:shapelayout></xml><![endif]--></head><body lang=3DEN-US link=3Dblue =
vlink=3Dpurple><div class=3DWordSection1><p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri",sans-serif'>> =
Ignoring hardware and software demands for the moment is it =
preferable/practical/wise to optimize such a =
structure?<o:p></o:p></span></p><p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri",sans-serif'><o:p> </=
o:p></span></p><p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri",sans-serif'>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.<o:p></o:p></span></p><p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri",sans-serif'><o:p> </=
o:p></span></p><p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri",sans-serif'>Jim<o:p></o:p=
></span></p><p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri",sans-serif'><o:p> </=
o:p></span></p><p class=3DMsoNormal><b><span =
style=3D'font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span><=
/b><span style=3D'font-size:11.0pt;font-family:"Calibri",sans-serif'> =
owner-chemistry+jimkress35=3D=3Dgmail.com!A!ccl.net =
[mailto:owner-chemistry+jimkress35=3D=3Dgmail.com!A!ccl.net] <b>On Behalf =
Of </b>John McKelvey jmmckel*gmail.com<br><b>Sent:</b> Wednesday, =
January 04, 2017 12:17 PM<br><b>To:</b> Kress, Jim =
<jimkress35!A!gmail.com><br><b>Subject:</b> CCL: Protein =
structures<o:p></o:p></span></p><p =
class=3DMsoNormal><o:p> </o:p></p><div><div><div><div><p =
class=3DMsoNormal =
style=3D'margin-bottom:12.0pt'>Folks,<o:p></o:p></p></div><p =
class=3DMsoNormal style=3D'margin-bottom:12.0pt'>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?<o:p></o:p></p></div><p class=3DMsoNormal =
style=3D'margin-bottom:12.0pt'>Many thanks!<o:p></o:p></p></div><p =
class=3DMsoNormal>John<br =
clear=3Dall><o:p></o:p></p><div><div><div><div><p =
class=3DMsoNormal><br>-- <o:p></o:p></p><div><div><div><div><div><p =
class=3DMsoNormal>John McKelvey<br>545 Legacy Pointe =
Dr<o:p></o:p></p></div><div><p class=3DMsoNormal>O'Fallon, MO =
63376<br>636-294-5203<br><a href=3D"mailto:jmmckel%7b:%7dgmail.com" =
target=3D"_blank">jmmckel{:}gmail.com</a><o:p></o:p></p></div></div></div=
></div></div></div></div></div></div></div></div></body></html>
------=_NextPart_000_01A2_01D266A9.7AC67BA0--
From owner-chemistry@ccl.net Wed Jan 4 21:16:00 2017
From: "Gregory L Warren greg#,#eyesopen.com" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL: Protein structures
Message-Id: <-52582-170104185826-22000-BDDhWlMwPqZH5LkqbGhcTw^^^server.ccl.net>
X-Original-From: "Gregory L Warren" <greg,+,eyesopen.com>
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 <greg^^eyesopen.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
From owner-chemistry@ccl.net Wed Jan 4 22:37:00 2017
From: "Lars Goerigk lars.goerigk#unimelb.edu.au" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: Protein structures
Message-Id: <-52583-170104205328-26276-HEchTXI1ow5fq8yfLINZtQ{=}server.ccl.net>
X-Original-From: Lars Goerigk <lars.goerigk=unimelb.edu.au>
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<http://www.chemistry.unimelb.edu.=
au/dr-lars-goerigk>
Follow me on Twitter: https://twitter.com/lgoer_compchem
On 5 Jan 2017, at 8:42 am, Jim Kress jimkress35. : .gmail.com<http://gmail.co=
m> <owner-chemistry : ccl.net<mailto:owner-chemistry : ccl.net>> 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<http://gmail.com/>]![ccl.ne=
t<http://ccl.net/> [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com<http:/=
/gmail.com/>]![ccl.net<http://ccl.net/>] On Behalf Of John McKelvey jmmckel=
*gmail.com<http://gmail.com>
Sent: Wednesday, January 04, 2017 12:17 PM
To: Kress, Jim <jimkress35]![gmail.com<http://gmail.com>>
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<mailto:jmmckel%7b:%7dgmail.com>
--_000_CE24172FE0564E6A85FC62F2AE46F1C3unimelbeduau_
Content-Type: text/html; charset=WINDOWS-1252
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<html>
<head>
<meta http-equiv=3D"Content-Type" content=3D"text/html; charset=3Dus-ascii"=
>
</head>
<body style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-lin=
e-break: after-white-space;">
Hi John,
<div><br>
</div>
<div>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</div>
<div><br>
</div>
<div>J. Phys Chem B 2014, <em>118</em>, 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.</div>
<div><br>
</div>
<div>Best wishes,</div>
<div><br>
</div>
<div>Lars</div>
<div>
<div>
<div style=3D"color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; t=
ext-align: start; text-indent: 0px; text-transform: none; white-space: norm=
al; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-w=
rap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-=
space;">
<div style=3D"color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; t=
ext-align: start; text-indent: 0px; text-transform: none; white-space: norm=
al; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-w=
rap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-=
space;">
<div style=3D"color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; t=
ext-align: start; text-indent: 0px; text-transform: none; white-space: norm=
al; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-w=
rap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-=
space;">
<div style=3D"color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; t=
ext-align: start; text-indent: 0px; text-transform: none; white-space: norm=
al; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-w=
rap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-=
space;">
<div style=3D"color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; t=
ext-align: start; text-indent: 0px; text-transform: none; white-space: norm=
al; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-w=
rap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-=
space;">
<div style=3D"color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; t=
ext-align: start; text-indent: 0px; text-transform: none; white-space: norm=
al; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-w=
rap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-=
space;">
<div style=3D"color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; t=
ext-align: start; text-indent: 0px; text-transform: none; white-space: norm=
al; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-w=
rap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-=
space;">
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;=
font-style: normal; font-variant: normal; font-weight: normal; letter-spac=
ing: normal; line-height: normal; orphans: auto; text-align: start; text-in=
dent: 0px; text-transform: none; white-space: normal; widows: auto; word-sp=
acing: 0px; -webkit-text-stroke-width: 0px;">
<br class=3D"Apple-interchange-newline">
<br>
</div>
<div style=3D"color: rgb(0, 0, 0); font-variant: normal; letter-spacing: no=
rmal; line-height: normal; orphans: auto; text-align: start; text-indent: 0=
px; text-transform: none; white-space: normal; widows: auto; word-spacing: =
0px; -webkit-text-stroke-width: 0px;">
<span style=3D"font-size: 14px;"><b>Dr Lars Goerigk<span class=3D"Apple-con=
verted-space"> </span></b>|</span><b style=3D"font-family: Helvetica; =
font-size: 12px; font-weight: normal; font-style: normal;"> </b><span =
style=3D"font-size: 14px;">Lecturer & ARC DECRA Fellow</span></div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;=
font-style: normal; font-variant: normal; font-weight: normal; letter-spac=
ing: normal; line-height: normal; orphans: auto; text-align: start; text-in=
dent: 0px; text-transform: none; white-space: normal; widows: auto; word-sp=
acing: 0px; -webkit-text-stroke-width: 0px;">
School of Chemistry | The University of Melbourne</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;=
font-style: normal; font-variant: normal; font-weight: normal; letter-spac=
ing: normal; line-height: normal; orphans: auto; text-align: start; text-in=
dent: 0px; text-transform: none; white-space: normal; widows: auto; word-sp=
acing: 0px; -webkit-text-stroke-width: 0px;">
Victoria 3010 | Australia</div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;=
font-style: normal; font-variant: normal; font-weight: normal; letter-spac=
ing: normal; line-height: normal; orphans: auto; text-align: start; text-in=
dent: 0px; text-transform: none; white-space: normal; widows: auto; word-sp=
acing: 0px; -webkit-text-stroke-width: 0px;">
<i>Website: </i><a href=3D"http://www.chemistry.unimelb.edu.au/dr-lars=
-goerigk">goerigk.chemistry.unimelb.edu.au</a></div>
<div style=3D"color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;=
font-style: normal; font-variant: normal; font-weight: normal; letter-spac=
ing: normal; line-height: normal; orphans: auto; text-align: start; text-in=
dent: 0px; text-transform: none; white-space: normal; widows: auto; word-sp=
acing: 0px; -webkit-text-stroke-width: 0px;">
<i>Follow me on Twitter: </i><span style=3D"font-style: normal;"><a hr=
ef=3D"https://twitter.com/lgoer_compchem">https://twitter.com/lgoer_compche=
m</a></span></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<div>
<div>On 5 Jan 2017, at 8:42 am, Jim Kress jimkress35. : .<a href=3D"http://gm=
ail.com">gmail.com</a> <<a href=3D"mailto:owner-chemistry : ccl.net">owner=
-chemistry : ccl.net</a>> wrote:</div>
<br class=3D"Apple-interchange-newline">
<blockquote type=3D"cite">
<div lang=3D"EN-US" link=3D"blue" vlink=3D"purple" style=3D"font-family: He=
lvetica; font-size: 12px; font-style: normal; font-variant: normal; font-we=
ight: normal; letter-spacing: normal; line-height: normal; orphans: auto; t=
ext-align: start; text-indent: 0px; text-transform: none; white-space: norm=
al; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<div class=3D"WordSection1" style=3D"page: WordSection1;">
<div style=3D"margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Time=
s New Roman', serif;">
<span style=3D"font-size: 11pt; font-family: Calibri, sans-serif;">> Ign=
oring hardware and software demands for the moment is it preferable/practic=
al/wise to optimize such a structure?<o:p></o:p></span></div>
<div style=3D"margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Time=
s New Roman', serif;">
<span style=3D"font-size: 11pt; font-family: Calibri, sans-serif;"> </=
span></div>
<div style=3D"margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Time=
s New Roman', serif;">
<span style=3D"font-size: 11pt; font-family: Calibri, sans-serif;">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.<o:p></o:p></span></div>
<div style=3D"margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Time=
s New Roman', serif;">
<span style=3D"font-size: 11pt; font-family: Calibri, sans-serif;"> </=
span></div>
<div style=3D"margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Time=
s New Roman', serif;">
<span style=3D"font-size: 11pt; font-family: Calibri, sans-serif;">Jim<o:p>=
</o:p></span></div>
<div style=3D"margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Time=
s New Roman', serif;">
<span style=3D"font-size: 11pt; font-family: Calibri, sans-serif;"> </=
span></div>
<div style=3D"margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Time=
s New Roman', serif;">
<b><span style=3D"font-size: 11pt; font-family: Calibri, sans-serif;">From:=
</span></b><span style=3D"font-size: 11pt; font-family: Calibri, sans-serif=
;"><span class=3D"Apple-converted-space"> </span>owner-chemistry+jimkr=
ess35=3D=3D<a href=3D"http://gmail.com/" style=3D"color: purple; text-decor=
ation: underline;">gmail.com</a>]![<a href=3D"http://ccl.net/" style=3D"col=
or: purple; text-decoration: underline;">ccl.net</a><span class=3D"Apple-co=
nverted-space"> </span>[mailto:owner-chemistry+jimkress35=3D=3D<a href=
=3D"http://gmail.com/" style=3D"color: purple; text-decoration: underline;"=
>gmail.com</a>]![<a href=3D"http://ccl.net/" style=3D"color: purple; text-d=
ecoration: underline;">ccl.net</a>]<span class=3D"Apple-converted-space">&n=
bsp;</span><b>On
Behalf Of<span class=3D"Apple-converted-space"> </span></b>John McKel=
vey jmmckel*<a style=3D"color: purple; text-decoration: underline;" href=3D=
"http://gmail.com">gmail.com</a><br>
<b>Sent:</b><span class=3D"Apple-converted-space"> </span>Wednesday, J=
anuary 04, 2017 12:17 PM<br>
<b>To:</b><span class=3D"Apple-converted-space"> </span>Kress, Jim <=
;jimkress35]![<a style=3D"color: purple; text-decoration: underline;" href=
=3D"http://gmail.com">gmail.com</a>><br>
<b>Subject:</b><span class=3D"Apple-converted-space"> </span>CCL: Prot=
ein structures<o:p></o:p></span></div>
<div style=3D"margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Time=
s New Roman', serif;">
<o:p> </o:p></div>
<div>
<div>
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<div>
<p class=3D"MsoNormal" style=3D"margin: 0in 0in 12pt; font-size: 12pt; font=
-family: 'Times New Roman', serif;">
Folks,<o:p></o:p></p>
</div>
<p class=3D"MsoNormal" style=3D"margin: 0in 0in 12pt; font-size: 12pt; font=
-family: 'Times New Roman', serif;">
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?<o:p></o:p></p>
</div>
<p class=3D"MsoNormal" style=3D"margin: 0in 0in 12pt; font-size: 12pt; font=
-family: 'Times New Roman', serif;">
Many thanks!<o:p></o:p></p>
</div>
<div style=3D"margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Time=
s New Roman', serif;">
John<br clear=3D"all">
<o:p></o:p></div>
<div>
<div style=3D"margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Time=
s New Roman', serif;">
<br>
--<o:p></o:p></div>
<div>
<div>
<div style=3D"margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Time=
s New Roman', serif;">
John McKelvey<br>
545 Legacy Pointe Dr<o:p></o:p></div>
</div>
<div>
<div style=3D"margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: 'Time=
s New Roman', serif;">
O'Fallon, MO 63376<br>
636-294-5203<br>
<a href=3D"mailto:jmmckel%7b:%7dgmail.com" target=3D"_blank" style=3D"color=
: purple; text-decoration: underline;">jmmckel{:}gmail.com</a></div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
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