id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5912 Crash handling tool window closeEvent after AlphaFold prediction finishes chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""libopenblas.0.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703290822656, ""size"" : 290816, ""uuid"" : ""be53a13c-8ce1-3e40-b9bc-98473d3eed3e"", ""path"" : ""\/usr\/lib\/system\/libdispatch.dylib"", ""name"" : ""libdispatch.dylib"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703415828480, ""CFBundleShortVersionString"" : ""1.11"", ""CFBundleIdentifier"" : ""com.apple.QuartzCore"", ""size"" : 3047424, ""uuid"" : ""7e85dee1-5bb8-3ac2-ad98-2552838e01ca"", ""path"" : ""\/System\/Library\/Frameworks\/QuartzCore.framework\/Versions\/A\/QuartzCore"", ""name"" : ""QuartzCore"", ""CFBundleVersion"" : ""962.57.1"" } ], ""sharedCache"" : { ""base"" : 140703289376768, ""size"" : 15215640576, ""uuid"" : ""b5084610-afe4-3485-bade-628c4468b057"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=3.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 2176K 4 \nCG image 700K 70 \nColorSync 240K 28 \nCoreAnimation 9096K 107 \nCoreGraphics 12K 2 \nCoreUI image data 5244K 42 \nFoundation 48K 2 \nKernel Alloc Once 12K 2 \nMALLOC 1.8G 459 \nMALLOC guard page 192K 8 \nMALLOC_MEDIUM (reserved) 664.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 40K 10 \nOpenGL GLSL 384K 5 \nRosetta Arena 4096K 2 \nRosetta Generic 2128K 529 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 1040K 104 \nRosetta Thread Context 1040K 104 \nSTACK GUARD 64K 16 \nStack 176.3M 52 \nStack Guard 56.2M 36 \nVM_ALLOCATE 140.7M 493 \nVM_ALLOCATE (reserved) 160.1M 14 reserved VM address space (unallocated)\n__DATA 43.5M 754 \n__DATA_CONST 30.0M 342 \n__DATA_DIRTY 1641K 218 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 797.4M 207 \n__OBJC_RO 81.6M 1 \n__OBJC_RW 3120K 2 \n__TEXT 813.0M 730 \n__UNICODE 588K 1 \ndyld private memory 1024K 1 \nmapped file 5.6G 1330 \nshared memory 3180K 33 \nunshared pmap 10.5M 8 \n=========== ======= ======= \nTOTAL 10.6G 5732 \nTOTAL, minus reserved VM space 9.7G 5732 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""607844aa04477260f58a8077"", ""factorPackIds"" : { ""SIRI_MORPHUN_ASSETS"" : ""6103050cbfe6dc472e1c982a"" }, ""deploymentId"" : 240000066 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""602ad4dac86151000cf27e46"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""61ae8d06da72d16a4beb762e"" }, ""deploymentId"" : 240000290 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000090 }, { ""rolloutId"" : ""5fc94383418129005b4e9ae0"", ""factorPackIds"" : { }, ""deploymentId"" : 240000207 }, { ""rolloutId"" : ""601d9415f79519000ccd4b69"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""61c0d3122be4e338e11ae9e1"" }, ""deploymentId"" : 240000362 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/chenyang/Downloads/ChimeraX/AlphaFold/prediction_2/best_model_545.pdb > format pdb Chain information for best_model_545.pdb #1 --- Chain | Description A | No description available > select clear Drag select of 42 residues > mlp sel Map values for surface ""best_model_545.pdb_A SES surface"": minimum -25.35, mean -4.154, maximum 25.38 To also show corresponding color key, enter the above mlp command and add key true > select clear > hide surfaces Alignment identifier is 1/A > select /A:169 22 atoms, 22 bonds, 1 residue, 1 model selected > select /A:152-169 301 atoms, 302 bonds, 18 residues, 1 model selected > select /A:147 24 atoms, 25 bonds, 1 residue, 1 model selected > select /A:147-151 86 atoms, 87 bonds, 5 residues, 1 model selected > mlp sel Map values for surface ""best_model_545.pdb_A SES surface"": minimum -25.35, mean -4.154, maximum 25.38 To also show corresponding color key, enter the above mlp command and add key true > select clear > select /A:146 15 atoms, 14 bonds, 1 residue, 1 model selected > select /A:1-146 2364 atoms, 2382 bonds, 146 residues, 1 model selected > hide target m > show target m > delete sel > select clear Drag select of best_model_545.pdb_A SES surface, 11235 of 51156 triangles, 23 residues > select clear Drag select of best_model_545.pdb_A SES surface, 11235 of 51156 triangles, 23 residues > mlp sel Map values for surface ""best_model_545.pdb_A SES surface"": minimum -23.49, mean -1.825, maximum 22.32 To also show corresponding color key, enter the above mlp command and add key true > undo > show target m > hide target m > show target m > close > open > /Users/chenyang/Downloads/ChimeraX/AlphaFold/prediction_2/best_model_545.pdb > format pdb Chain information for best_model_545.pdb #1 --- Chain | Description A | No description available > select add /A:169 22 atoms, 22 bonds, 1 residue, 1 model selected > select add /A:167 36 atoms, 35 bonds, 2 residues, 1 model selected > select add /A:168 60 atoms, 58 bonds, 3 residues, 1 model selected Drag select of 12 residues > select add /A:166 274 atoms, 76 bonds, 16 residues, 1 model selected Drag select of 9 residues Drag select of 6 residues > select subtract /A:1 433 atoms, 76 bonds, 26 residues, 1 model selected Drag select of 2 residues > select add /A:144 417 atoms, 90 bonds, 25 residues, 1 model selected > select add /A:143 433 atoms, 105 bonds, 26 residues, 1 model selected > select add /A:141 455 atoms, 126 bonds, 27 residues, 1 model selected > ui tool show Contacts > contacts sel reveal true log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 270 contacts atom1 atom2 overlap distance /A LYS 141 HZ1 /A ASP 137 OD1 0.387 1.693 /A TRP 147 HE1 /A VAL 143 HG23 0.347 1.653 /A PRO 163 C /A GLU 165 H 0.325 2.375 /A VAL 143 CG2 /A TRP 147 HE1 0.318 2.382 /A ARG 159 HH21 /A PRO 20 HB3 0.317 1.683 /A TRP 147 HD1 /A VAL 143 O 0.314 2.166 /A TRP 147 HH2 /A ILE 14 CD1 0.309 2.391 /A VAL 143 O /A GLU 146 H 0.285 1.795 /A PRO 163 O /A GLU 165 H 0.277 1.803 /A TYR 169 O /A ARG 57 HH22 0.265 1.815 /A SER 151 H /A GLU 154 OE2 0.259 1.821 /A GLU 157 H /A GLU 153 O 0.252 1.828 /A THR 167 CG2 /A TYR 169 CE2 0.222 3.178 /A SER 151 HG /A GLU 154 OE2 0.215 1.865 /A SER 151 HG /A GLU 154 CD 0.184 2.516 /A SER 151 O /A ILE 155 H 0.160 1.920 /A TRP 147 NE1 /A VAL 143 CG2 0.157 3.168 /A TRP 147 CD1 /A GLU 144 HA 0.144 2.556 /A LEU 164 C /A ILE 166 H 0.143 2.557 /A LYS 141 CE /A ASP 137 OD1 0.124 3.056 /A THR 167 CG2 /A TYR 169 CZ 0.077 3.323 /A LYS 141 NZ /A ASP 137 OD1 0.066 2.639 /A GLU 156 H /A ASP 152 O 0.064 2.016 /A ILE 155 CD1 /A LEU 19 CD1 0.064 3.336 /A VAL 150 CG1 /A GLU 154 CB 0.062 3.338 /A GLU 144 C /A GLU 146 H 0.056 2.644 /A GLU 165 C /A THR 167 H 0.052 2.648 /A VAL 143 HG21 /A ALA 139 O 0.044 2.436 /A TYR 169 C /A ARG 57 HH22 0.042 2.658 /A TRP 147 HZ3 /A ILE 25 CD1 0.041 2.659 /A SER 151 C /A GLU 153 H 0.037 2.663 /A TYR 169 O /A ARG 57 NH2 0.033 2.672 /A TRP 147 CD1 /A VAL 143 O 0.032 3.148 /A ALA 158 CB /A LEU 43 O 0.028 3.152 /A VAL 143 HG23 /A ALA 140 O 0.026 2.454 /A TRP 147 CH2 /A ILE 14 CD1 0.025 3.375 /A VAL 143 HG13 /A LEU 1 CD2 0.023 2.677 /A GLU 156 O /A ARG 159 HB2 0.022 2.458 /A GLU 156 O /A GLN 160 H 0.017 2.063 /A ALA 158 HB3 /A LEU 43 O 0.015 2.465 /A TRP 147 NE1 /A VAL 143 HG23 0.012 2.613 /A SER 151 HG /A GLU 154 CG 0.010 2.690 /A TYR 169 CE2 /A THR 167 HG22 0.002 2.698 /A ALA 158 H /A GLU 154 O 0.002 2.078 /A ARG 159 HH21 /A PRO 20 CB -0.004 2.704 /A VAL 143 CG1 /A LEU 1 O -0.012 3.192 /A PRO 163 O /A GLU 165 N -0.020 2.725 /A ILE 155 O /A ARG 159 HG2 -0.026 2.506 /A ILE 155 O /A ARG 159 H -0.027 2.107 /A VAL 150 O /A SER 151 O -0.029 2.989 /A TRP 147 CD1 /A GLU 144 CA -0.029 3.429 /A THR 167 H /A GLU 165 O -0.032 2.112 /A VAL 143 HG12 /A LEU 1 O -0.033 2.513 /A ARG 159 NH2 /A PRO 20 HB3 -0.034 2.659 /A VAL 143 O /A GLU 146 N -0.037 2.742 /A TRP 147 CZ3 /A ILE 25 CD1 -0.042 3.442 /A GLU 156 O /A GLN 160 HG3 -0.044 2.524 /A LYS 141 H /A ASP 137 O -0.045 2.125 /A ASP 152 O /A GLU 156 CB -0.047 3.227 /A VAL 148 N /A GLU 146 O -0.054 2.759 /A ARG 159 NH2 /A PRO 20 O -0.062 2.767 /A VAL 143 C /A TRP 147 HD1 -0.064 2.764 /A TYR 169 O /A ARG 57 CZ -0.065 3.245 /A TRP 147 O /A ILE 149 N -0.069 2.774 /A TRP 147 HZ2 /A ALA 140 CB -0.073 2.773 /A TRP 147 HH2 /A ILE 14 HD13 -0.075 2.075 /A VAL 143 C /A GLU 146 H -0.076 2.776 /A VAL 143 O /A GLU 146 CB -0.076 3.256 /A SER 151 N /A GLU 154 OE2 -0.077 2.782 /A SER 151 OG /A GLU 154 CG -0.080 3.280 /A ILE 155 CD1 /A LEU 19 HD13 -0.082 2.782 /A LYS 161 O /A PRO 163 HD2 -0.082 2.562 /A TYR 169 CE2 /A THR 167 HG21 -0.085 2.785 /A ILE 149 H /A TRP 147 O -0.087 2.167 /A VAL 143 CG2 /A ALA 139 O -0.092 3.272 /A TRP 147 HH2 /A ILE 14 CG2 -0.094 2.794 /A GLU 142 HG3 /A GLU 138 O -0.100 2.580 /A VAL 143 O /A GLU 146 HB3 -0.102 2.582 /A TRP 147 HH2 /A ILE 14 HG23 -0.104 2.104 /A VAL 143 C /A TRP 147 CD1 -0.104 3.504 /A GLU 157 O /A LYS 161 H -0.105 2.185 /A VAL 150 O /A ILE 149 HG22 -0.106 2.586 /A TYR 169 CZ /A THR 167 HG21 -0.106 2.806 /A LYS 141 HZ1 /A ASP 137 CG -0.110 2.810 /A GLU 153 O /A GLU 157 N -0.110 2.815 /A ILE 155 O /A ARG 159 CG -0.113 3.293 /A VAL 150 O /A ILE 155 CD1 -0.123 3.303 /A TRP 147 HH2 /A ILE 14 HD12 -0.124 2.124 /A TRP 147 CH2 /A ILE 14 HG23 -0.126 2.826 /A GLU 153 O /A GLU 157 HG3 -0.126 2.606 /A VAL 150 CG1 /A GLU 154 HB2 -0.128 2.828 /A TRP 147 C /A ILE 149 H -0.130 2.830 /A VAL 150 HG12 /A GLU 154 CB -0.132 2.832 /A ILE 149 O /A SER 151 N -0.137 2.842 /A TRP 147 HH2 /A ILE 14 CB -0.141 2.841 /A ASP 152 O /A GLU 156 HB3 -0.143 2.623 /A GLU 142 HB3 /A ALA 139 O -0.144 2.624 /A VAL 143 HG13 /A LEU 1 HD21 -0.147 2.147 /A SER 151 OG /A GLU 154 HG2 -0.151 2.651 /A ILE 155 HD13 /A LEU 19 HD13 -0.152 2.152 /A TRP 147 H /A GLU 144 O -0.157 2.237 /A ILE 155 HG12 /A VAL 150 HG12 -0.159 2.159 /A LYS 161 O /A PRO 163 CD -0.163 3.343 /A VAL 150 HG12 /A GLU 154 HB2 -0.165 2.165 /A ILE 155 HG12 /A SER 151 O -0.168 2.648 /A ARG 159 HH21 /A PRO 20 C -0.171 2.871 /A SER 151 O /A GLU 154 N -0.172 2.877 /A SER 151 OG /A GLU 154 H -0.172 2.272 /A VAL 150 CG1 /A GLU 154 HB3 -0.174 2.874 /A GLU 144 OE1 /A TYR 105 HE2 -0.178 2.658 /A TRP 147 HZ2 /A LEU 5 HD12 -0.182 2.182 /A LYS 161 O /A PRO 163 N -0.182 3.287 /A TYR 169 OH /A THR 167 HG21 -0.182 2.682 /A LYS 141 HB2 /A GLU 138 O -0.183 2.663 /A LYS 141 CE /A ARG 97 O -0.184 3.364 /A TRP 147 CH2 /A ILE 14 CG2 -0.186 3.586 /A GLU 144 C /A TRP 147 H -0.187 2.887 /A TYR 169 C /A ARG 57 NH2 -0.189 3.514 /A VAL 143 O /A GLU 146 CA -0.190 3.370 /A TYR 169 CZ /A THR 167 HG22 -0.193 2.893 /A ARG 159 HH21 /A PRO 20 O -0.193 2.273 /A PRO 163 HD2 /A ALA 162 HA -0.193 2.193 /A GLU 165 O /A THR 167 N -0.195 2.900 /A VAL 150 HG13 /A GLU 154 CB -0.196 2.896 /A SER 151 OG /A GLU 154 CD -0.199 3.399 /A VAL 148 H /A GLU 146 O -0.201 2.281 /A LYS 141 CG /A ASP 137 O -0.204 3.384 /A TRP 147 CH2 /A ILE 14 HD13 -0.204 2.904 /A SER 151 O /A ILE 155 N -0.207 2.912 /A TRP 147 CZ2 /A LEU 5 HD12 -0.207 2.907 /A LYS 141 HE3 /A ARG 97 O -0.208 2.688 /A TRP 147 CZ2 /A LEU 5 CD1 -0.210 3.610 /A TRP 147 NE1 /A VAL 143 HG22 -0.211 2.836 /A ALA 158 O /A ALA 162 H -0.213 2.293 /A GLU 156 O /A GLN 160 CG -0.214 3.394 /A GLU 156 HG3 /A GLN 160 NE2 -0.215 2.840 /A SER 151 C /A GLU 154 H -0.218 2.918 /A ILE 155 HD12 /A LEU 19 CD1 -0.220 2.920 /A TRP 147 NE1 /A GLU 144 HA -0.222 2.847 /A VAL 143 CG1 /A LEU 1 CD2 -0.223 3.623 /A GLU 156 O /A ARG 159 CB -0.226 3.406 /A VAL 143 CG1 /A LEU 1 HD21 -0.227 2.927 /A ALA 158 CB /A GLU 154 O -0.228 3.408 /A LYS 141 C /A GLU 144 H -0.230 2.930 /A TRP 147 CE3 /A ILE 25 HD12 -0.231 2.931 /A ILE 166 H /A LEU 164 O -0.231 2.311 /A ILE 155 HD13 /A LEU 19 CD1 -0.231 2.931 /A LYS 141 CD /A ASP 137 OD1 -0.233 3.413 /A ARG 168 HG3 /A ILE 166 HG21 -0.235 2.235 /A LYS 141 HG2 /A ASP 137 O -0.235 2.715 /A LYS 141 C /A VAL 143 H -0.236 2.936 /A VAL 143 CG2 /A ALA 140 HA -0.240 2.940 /A SER 151 OG /A GLU 154 OE2 -0.243 2.823 /A TYR 169 OH /A PRO 53 HG3 -0.243 2.743 /A ILE 155 CD1 /A LEU 19 HD12 -0.244 2.944 /A TRP 147 HE3 /A ILE 25 HD12 -0.246 2.246 /A GLU 144 HB2 /A ALA 140 O -0.249 2.729 /A ASP 152 O /A GLU 156 N -0.249 2.954 /A VAL 150 HA /A GLU 154 OE2 -0.250 2.730 /A LYS 141 HE2 /A ASP 137 OD1 -0.251 2.731 /A TRP 147 H /A GLU 145 C -0.254 2.954 /A ILE 155 HG12 /A VAL 150 CG1 -0.254 2.954 /A SER 151 O /A GLU 154 HB2 -0.255 2.735 /A VAL 148 O /A VAL 150 N -0.261 2.966 /A GLU 142 H /A GLU 138 O -0.262 2.342 /A SER 151 N /A GLU 154 HB2 -0.262 2.887 /A VAL 150 HG12 /A ILE 155 N -0.265 2.890 /A GLU 144 N /A ALA 140 O -0.267 2.972 /A TRP 147 O /A ILE 149 HG12 -0.268 2.748 /A VAL 143 CG1 /A LEU 1 C -0.269 3.669 /A SER 151 O /A GLU 154 H -0.271 2.351 /A GLU 157 O /A LYS 161 HG2 -0.276 2.756 /A GLU 157 O /A LYS 161 CG -0.277 3.457 /A GLU 156 HA /A ARG 159 HD2 -0.277 2.277 /A VAL 143 C /A GLU 145 H -0.283 2.983 /A TRP 147 HZ3 /A ILE 25 CG1 -0.284 2.984 /A TRP 147 HZ3 /A ILE 25 HD13 -0.286 2.286 /A GLU 153 O /A GLU 157 CG -0.287 3.467 /A SER 151 O /A GLU 153 N -0.287 2.992 /A TRP 147 HZ2 /A ALA 140 HB3 -0.287 2.287 /A VAL 150 O /A ILE 155 HD12 -0.288 2.768 /A TRP 147 CE3 /A ILE 25 CD1 -0.290 3.690 /A ASP 152 O /A ILE 155 HB -0.292 2.772 /A GLU 153 C /A GLU 157 H -0.295 2.995 /A GLU 156 HG3 /A GLN 160 HE22 -0.300 2.300 /A ILE 166 C /A ARG 168 H -0.301 3.001 /A TYR 169 CD2 /A THR 167 HG22 -0.302 3.002 /A VAL 150 HG13 /A GLU 154 HB3 -0.303 2.303 /A GLU 144 O /A TRP 147 HB3 -0.305 2.785 /A ILE 155 O /A ALA 158 HB1 -0.305 2.785 /A ARG 159 NH2 /A PRO 20 C -0.305 3.630 /A SER 151 H /A GLU 154 CD -0.306 3.006 /A LYS 161 H /A ARG 159 C -0.306 3.006 /A SER 151 HG /A GLU 154 HG2 -0.308 2.308 /A ILE 166 CG2 /A ARG 168 HG3 -0.308 3.008 /A VAL 143 H /A ALA 140 C -0.308 3.008 /A GLU 156 O /A GLN 160 N -0.309 3.014 /A GLN 160 H /A GLU 157 C -0.309 3.009 /A TRP 147 CZ3 /A ILE 25 HD13 -0.312 3.012 /A TRP 147 CZ2 /A ALA 140 CB -0.313 3.713 /A ILE 149 O /A VAL 150 O -0.313 3.273 /A THR 167 CG2 /A TYR 169 OH -0.314 3.514 /A ARG 168 CG /A ILE 166 HG21 -0.315 3.015 /A TRP 147 CZ2 /A ALA 140 HB3 -0.315 3.015 /A SER 151 CB /A GLU 154 OE2 -0.316 3.496 /A GLU 153 O /A GLU 157 CB -0.319 3.499 /A ARG 159 H /A GLU 156 C -0.321 3.021 /A GLU 144 CA /A ALA 140 O -0.322 3.502 /A TRP 147 CH2 /A ILE 14 HD12 -0.322 3.022 /A GLU 157 O /A GLN 160 HB2 -0.323 2.803 /A ILE 166 O /A ARG 168 N -0.324 3.029 /A VAL 150 O /A ILE 155 HG12 -0.324 2.804 /A TRP 147 HD1 /A GLU 144 CA -0.324 3.024 /A VAL 143 CG2 /A ALA 140 O -0.325 3.505 /A ILE 155 CG1 /A VAL 150 CG1 -0.327 3.727 /A TRP 147 HH2 /A ILE 14 CG1 -0.328 3.028 /A GLU 142 H /A ALA 139 C -0.329 3.029 /A TRP 147 CZ3 /A ILE 25 HD12 -0.329 3.029 /A ARG 159 H /A GLU 157 C -0.330 3.030 /A ILE 155 O /A ARG 159 N -0.332 3.037 /A GLU 156 H /A GLU 153 C -0.332 3.032 /A TYR 169 C /A ARG 57 CZ -0.333 3.733 /A LYS 141 HD3 /A ASP 137 OD1 -0.333 2.813 /A SER 151 O /A ILE 155 CG1 -0.334 3.514 /A ARG 168 H /A ILE 166 O -0.336 2.416 /A GLU 157 HB2 /A LYS 161 HZ2 -0.337 2.337 /A VAL 143 HG13 /A LEU 1 HD23 -0.338 2.338 /A GLU 144 H /A ALA 140 O -0.338 2.418 /A VAL 143 O /A GLU 145 N -0.339 3.044 /A SER 151 O /A GLU 154 CA -0.339 3.519 /A TRP 147 HZ3 /A ILE 25 HG12 -0.339 2.339 /A ILE 155 H /A GLU 153 C -0.340 3.040 /A TRP 147 HE1 /A VAL 143 HG22 -0.340 2.340 /A ALA 158 N /A GLU 154 O -0.343 3.048 /A GLU 153 O /A GLU 156 HB2 -0.343 2.823 /A ILE 149 O /A SER 151 CA -0.346 3.526 /A GLU 144 H /A GLU 142 C -0.346 3.046 /A ALA 162 H /A ARG 159 C -0.347 3.047 /A ASP 152 C /A GLU 156 H -0.350 3.050 /A SER 151 C /A GLU 154 N -0.355 3.680 /A SER 151 OG /A GLU 154 CB -0.356 3.556 /A GLU 157 HB3 /A GLU 154 O -0.356 2.836 /A THR 167 HG21 /A TYR 169 HH -0.357 2.357 /A TRP 147 HZ2 /A LEU 5 CD1 -0.358 3.058 /A LYS 161 H /A ALA 158 C -0.360 3.060 /A ALA 162 O /A PRO 163 O -0.361 3.321 /A ALA 158 HB2 /A GLU 154 O -0.365 2.845 /A ARG 159 NH2 /A PRO 20 CB -0.365 3.690 /A LYS 141 N /A ASP 137 O -0.369 3.074 /A TYR 169 C /A ARG 57 NE -0.373 3.698 /A ILE 166 CG2 /A ARG 168 CG -0.374 3.774 /A TRP 147 CD1 /A GLU 144 N -0.374 3.699 /A VAL 148 H /A GLU 146 C -0.375 3.075 /A VAL 143 HG23 /A ALA 140 HA -0.376 2.376 /A VAL 150 O /A ILE 155 CG1 -0.380 3.560 /A LYS 141 CB /A ASP 137 O -0.382 3.562 /A ILE 155 CG1 /A VAL 150 HG12 -0.382 3.082 /A VAL 143 HG23 /A ALA 140 C -0.384 3.084 /A TRP 147 H /A GLU 146 H -0.384 2.384 /A GLU 157 O /A LYS 161 N -0.388 3.093 /A GLU 144 CB /A ALA 140 O -0.389 3.569 /A THR 167 CG2 /A TYR 169 CD2 -0.391 3.791 /A SER 151 OG /A GLU 153 HB3 -0.392 2.892 /A VAL 143 C /A TRP 147 NE1 -0.393 3.718 /A GLU 142 CG /A GLU 138 O -0.396 3.576 /A TRP 147 CH2 /A ILE 14 CB -0.397 3.797 /A SER 151 HG /A GLU 154 CB -0.397 3.097 /A ARG 159 O /A ALA 162 HB3 -0.399 2.879 /A VAL 150 CA /A GLU 154 OE2 -0.399 3.579 /A LYS 141 NZ /A ASP 137 CG -0.400 3.725 270 contacts > select clear Alignment identifier is 1/A > select /A:5-7,29-35,39-42,47-50,57-68,119-146,152-161 1112 atoms, 1107 bonds, 89 pseudobonds, 68 residues, 2 models selected > select /A:146 15 atoms, 14 bonds, 1 residue, 1 model selected > select /A:143-146 61 atoms, 60 bonds, 9 pseudobonds, 4 residues, 2 models selected > select /A:147 24 atoms, 25 bonds, 1 residue, 1 model selected > select /A:147-150 75 atoms, 76 bonds, 7 pseudobonds, 4 residues, 2 models selected > close > open > /Users/chenyang/Downloads/ChimeraX/AlphaFold/prediction_1/best_model_539.pdb Chain information for best_model_539.pdb #1 --- Chain | Description A | No description available Drag select of 9 residues > select add /A:149 162 atoms, 18 bonds, 10 residues, 1 model selected > select add /A:151 177 atoms, 32 bonds, 11 residues, 1 model selected > select add /A:153 201 atoms, 55 bonds, 12 residues, 1 model selected > select add /A:152 211 atoms, 64 bonds, 13 residues, 1 model selected > select add /A:154 228 atoms, 80 bonds, 14 residues, 1 model selected > select add /A:155 250 atoms, 101 bonds, 15 residues, 1 model selected > select add /A:156 260 atoms, 110 bonds, 16 residues, 1 model selected Drag select of 8 residues > select add /A:156 387 atoms, 110 bonds, 23 residues, 1 model selected > delete sel Drag select of 2 residues > delete sel > mlp Map values for surface ""best_model_539.pdb_A SES surface"": minimum -25.4, mean -3.628, maximum 24.45 To also show corresponding color key, enter the above mlp command and add key true > hide surfaces > mlp Map values for surface ""best_model_539.pdb_A SES surface"": minimum -25.4, mean -3.628, maximum 24.45 To also show corresponding color key, enter the above mlp command and add key true > close > open > /Users/chenyang/Downloads/ChimeraX/AlphaFold/prediction_1/best_model_539.pdb > format pdb Chain information for best_model_539.pdb #1 --- Chain | Description A | No description available Drag select of 3 residues > select clear Drag select of 13 residues > select add /A:157 224 atoms, 14 bonds, 14 residues, 1 model selected > select add /A:156 234 atoms, 23 bonds, 15 residues, 1 model selected > select add /A:159 249 atoms, 37 bonds, 16 residues, 1 model selected > select add /A:160 268 atoms, 55 bonds, 17 residues, 1 model selected > select add /A:163 290 atoms, 77 bonds, 18 residues, 1 model selected > select add /A:162 314 atoms, 100 bonds, 19 residues, 1 model selected > select add /A:161 328 atoms, 113 bonds, 20 residues, 1 model selected > select add /A:143 347 atoms, 131 bonds, 21 residues, 1 model selected > select add /A:142 363 atoms, 146 bonds, 22 residues, 1 model selected > select add /A:141 387 atoms, 171 bonds, 23 residues, 1 model selected > ui tool show Contacts > contacts sel reveal true log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 220 contacts atom1 atom2 overlap distance /A TRP 141 CZ2 /A TYR 105 CE2 0.438 2.962 /A TRP 141 CH2 /A TYR 105 CE2 0.414 2.986 /A ILE 149 CG2 /A ARG 153 HE 0.413 2.287 /A LYS 155 HZ1 /A GLU 151 OE1 0.323 1.757 /A TRP 141 CE3 /A MET 96 CE 0.282 3.118 /A GLU 151 H /A GLU 147 O 0.254 1.826 /A TRP 141 CH2 /A TYR 105 CZ 0.185 3.215 /A TRP 141 CE3 /A MET 96 HE1 0.178 2.522 /A ILE 143 H /A GLU 140 O 0.163 1.917 /A ALA 152 CB /A ILE 25 HA 0.147 2.553 /A TRP 141 C /A ILE 143 H 0.146 2.554 /A GLN 154 HE22 /A GLU 150 OE1 0.122 1.958 /A ALA 152 H /A GLU 148 O 0.109 1.971 /A GLU 148 OE2 /A SER 145 HG 0.107 1.973 /A ARG 153 HE /A ILE 149 HG23 0.095 1.905 /A TRP 141 CD2 /A MET 96 CE 0.094 3.306 /A GLU 150 H /A ASP 146 O 0.093 1.987 /A THR 161 H /A ASP 21 CG 0.089 2.611 /A GLU 151 OE1 /A LYS 155 NZ 0.086 2.619 /A TRP 141 CH2 /A TYR 105 CD2 0.081 3.319 /A TRP 141 HH2 /A TYR 105 CZ 0.077 2.623 /A SER 145 C /A GLU 147 H 0.074 2.626 /A TRP 141 CD2 /A MET 96 HE3 0.070 2.630 /A GLU 148 CD /A SER 145 HG 0.070 2.630 /A GLU 150 O /A GLN 154 H 0.057 2.023 /A PRO 157 C /A GLU 159 H 0.053 2.647 /A PRO 157 O /A PRO 20 HB2 0.049 2.431 /A ILE 149 CG2 /A ARG 153 NE 0.046 3.279 /A THR 161 HB /A ASP 21 OD2 0.045 2.435 /A ARG 153 H /A ILE 149 O 0.037 2.043 /A ALA 156 HA /A GLY 44 O 0.017 2.463 /A LYS 155 HZ3 /A GLU 40 O 0.013 2.067 /A ILE 149 O /A ARG 153 HG3 0.007 2.473 /A TRP 141 CZ2 /A TYR 105 HE2 0.006 2.694 /A ILE 149 O /A ARG 153 CG -0.003 3.183 /A ARG 153 HB3 /A GLU 150 O -0.010 2.490 /A ILE 143 H /A GLU 140 C -0.022 2.722 /A GLU 148 CG /A SER 145 HG -0.025 2.725 /A ARG 153 NH2 /A ARG 18 NH2 -0.030 3.280 /A GLU 148 H /A SER 145 OG -0.036 2.136 /A ASP 146 O /A GLU 150 CB -0.036 3.216 /A TYR 163 HD2 /A ARG 48 CD -0.046 2.746 /A SER 145 OG /A GLU 148 CG -0.046 3.246 /A GLU 150 O /A GLN 154 HG2 -0.048 2.528 /A GLU 151 O /A LYS 155 H -0.050 2.130 /A TYR 163 HD2 /A ARG 48 HD3 -0.053 2.053 /A SER 145 O /A ILE 149 H -0.055 2.135 /A ALA 152 CB /A ILE 25 HG21 -0.057 2.757 /A GLU 151 OE1 /A LYS 155 CE -0.059 3.239 /A GLU 159 O /A PRO 157 HB3 -0.063 2.543 /A ILE 143 HB /A GLU 140 O -0.069 2.549 /A TRP 141 CZ3 /A MET 96 HE1 -0.073 2.773 /A ILE 160 HG13 /A ASP 21 H -0.075 2.075 /A TRP 141 CZ2 /A TYR 105 CZ -0.076 3.476 /A LYS 155 NZ /A GLU 40 HA -0.079 2.704 /A ALA 152 O /A ALA 156 H -0.082 2.162 /A LYS 155 CB /A GLY 44 HA2 -0.083 2.783 /A VAL 142 H /A GLU 140 C -0.087 2.787 /A GLU 148 O /A ALA 152 CB -0.090 3.270 /A TRP 141 CZ3 /A MET 96 CE -0.090 3.490 /A SER 145 OG /A GLU 148 HG3 -0.098 2.598 /A TYR 163 CD2 /A ARG 48 HD3 -0.103 2.803 /A ILE 160 HA /A ASP 21 HB2 -0.107 2.107 /A TRP 141 HZ3 /A ILE 14 HG22 -0.110 2.110 /A PRO 157 O /A PRO 20 CB -0.111 3.291 /A ILE 143 HD11 /A GLU 140 CG -0.114 2.814 /A GLU 147 O /A GLU 151 N -0.119 2.824 /A ILE 143 CB /A GLU 140 O -0.121 3.301 /A ILE 149 HG13 /A VAL 144 HG12 -0.122 2.122 /A GLU 148 CD /A PHE 26 HD2 -0.128 2.828 /A SER 145 H /A GLU 148 OE2 -0.128 2.208 /A ARG 153 NE /A ILE 149 HG23 -0.129 2.754 /A VAL 144 CG2 /A ILE 14 HD11 -0.131 2.831 /A GLN 154 HE22 /A GLU 150 CD -0.131 2.831 /A LYS 155 HZ3 /A GLU 40 C -0.132 2.832 /A TRP 141 HZ2 /A TYR 105 CE2 -0.134 2.834 /A GLU 151 CD /A LYS 155 HZ1 -0.135 2.835 /A ARG 153 HE /A ILE 149 HG21 -0.142 2.142 /A GLN 154 NE2 /A GLU 150 HG2 -0.143 2.768 /A TRP 141 CE3 /A MET 96 HE3 -0.148 2.848 /A THR 161 N /A ASP 21 CG -0.152 3.477 /A VAL 144 CG2 /A ILE 14 CD1 -0.153 3.553 /A ARG 153 CG /A LEU 19 HD11 -0.159 2.859 /A TRP 141 CE2 /A MET 96 HE3 -0.165 2.865 /A THR 161 CB /A ASP 21 OD2 -0.166 3.346 /A ILE 143 N /A GLU 140 O -0.167 2.872 /A TRP 141 HH2 /A TYR 105 CE2 -0.175 2.875 /A PRO 157 HD3 /A GLY 44 O -0.176 2.656 /A GLU 148 OE1 /A PHE 26 CD2 -0.178 3.358 /A LYS 155 NZ /A GLU 40 CA -0.180 3.505 /A GLU 150 O /A GLN 154 CG -0.181 3.361 /A TRP 141 CZ2 /A TYR 105 CD2 -0.184 3.584 /A ALA 152 CB /A ILE 25 CA -0.186 3.586 /A ALA 152 O /A ALA 156 N -0.188 2.893 /A ARG 153 HH22 /A ARG 18 NH2 -0.189 2.814 /A ASP 146 O /A GLU 150 HB2 -0.190 2.670 /A GLU 151 O /A LYS 155 HG3 -0.191 2.671 /A VAL 144 HG22 /A ILE 14 CD1 -0.195 2.895 /A ALA 152 O /A ALA 156 HB1 -0.195 2.675 /A ASP 146 O /A GLU 150 N -0.208 2.913 /A GLU 151 O /A GLN 154 HB2 -0.211 2.691 /A PRO 157 O /A PRO 20 CG -0.214 3.394 /A PRO 157 CB /A GLU 159 O -0.214 3.394 /A LEU 158 C /A GLU 159 HG3 -0.214 2.914 /A TYR 163 CD2 /A ARG 48 CD -0.215 3.615 /A ARG 153 NH1 /A LEU 19 HD23 -0.215 2.840 /A ARG 153 CG /A LEU 19 CD1 -0.217 3.617 /A ILE 143 O /A SER 145 N -0.224 2.929 /A LYS 155 HD3 /A LEU 43 O -0.226 2.706 /A ALA 156 CB /A PRO 23 HG3 -0.231 2.931 /A PRO 157 CD /A GLY 44 O -0.232 3.412 /A VAL 144 CG1 /A ILE 149 HG13 -0.233 2.933 /A LYS 155 CD /A LEU 43 O -0.234 3.414 /A ARG 153 HG2 /A LEU 19 CD1 -0.237 2.937 /A ILE 160 HG13 /A ASP 21 N -0.237 2.862 /A LYS 155 HZ3 /A GLU 40 CA -0.239 2.939 /A ILE 149 O /A ARG 153 N -0.242 2.947 /A ARG 153 CB /A GLU 150 O -0.244 3.424 /A GLU 148 OE1 /A PHE 26 HD2 -0.246 2.726 /A ILE 149 O /A ARG 153 CB -0.248 3.428 /A GLU 148 O /A ALA 152 N -0.251 2.956 /A ILE 149 HG12 /A ILE 25 HD11 -0.252 2.252 /A THR 161 H /A ASP 21 CB -0.254 2.954 /A GLU 147 O /A GLU 151 CB -0.254 3.434 /A ALA 156 H /A ARG 153 C -0.254 2.954 /A LEU 158 O /A GLU 159 CG -0.255 3.435 /A ALA 152 HB1 /A ILE 25 HA -0.255 2.255 /A GLU 151 O /A LYS 155 CG -0.255 3.435 /A GLN 154 NE2 /A GLU 150 OE1 -0.256 2.961 /A PRO 157 O /A PRO 20 HG3 -0.257 2.737 /A ALA 152 HB2 /A ILE 24 O -0.262 2.742 /A TRP 141 CZ3 /A ILE 14 HG22 -0.264 2.964 /A SER 145 OG /A GLU 148 CB -0.268 3.468 /A SER 145 OG /A GLU 148 CD -0.270 3.470 /A TRP 141 HZ2 /A TYR 105 HH -0.274 2.274 /A ILE 143 HD11 /A GLU 140 HG3 -0.275 2.275 /A ALA 152 O /A ALA 156 CB -0.276 3.456 /A ILE 143 CD1 /A GLU 140 HA -0.278 2.978 /A GLU 148 HB3 /A ILE 25 O -0.279 2.759 /A LYS 155 H /A ALA 152 C -0.280 2.980 /A ARG 153 H /A GLU 150 C -0.280 2.980 /A ARG 153 O /A ALA 156 HB2 -0.281 2.761 /A TRP 141 HH2 /A TYR 105 CE1 -0.281 2.981 /A GLU 150 O /A GLN 154 N -0.284 2.989 /A GLU 148 OE2 /A PHE 26 HD2 -0.286 2.766 /A ILE 160 HA /A ASP 21 CB -0.286 2.986 /A ARG 153 HG2 /A LEU 19 HD23 -0.290 2.290 /A ASP 146 O /A ILE 149 HB -0.292 2.772 /A VAL 144 HG22 /A ILE 14 HD11 -0.294 2.294 /A GLU 150 CG /A GLN 154 NE2 -0.294 3.619 /A LYS 155 HZ3 /A GLU 40 HA -0.294 2.294 /A GLU 148 OE1 /A PHE 26 CE2 -0.295 3.475 /A GLU 147 C /A GLU 151 H -0.296 2.996 /A ARG 153 HA /A LEU 19 HD13 -0.296 2.296 /A GLU 159 O /A PRO 157 CG -0.297 3.477 /A ALA 152 HB2 /A ILE 25 HG21 -0.297 2.297 /A VAL 144 CG1 /A ILE 149 CG1 -0.297 3.697 /A ILE 149 CG1 /A VAL 144 HG12 -0.298 2.998 /A GLU 150 HA /A ARG 153 HD3 -0.299 2.299 /A ILE 143 CA /A GLU 140 O -0.303 3.483 /A ALA 156 HA /A PRO 157 HD2 -0.309 2.309 /A LYS 155 HB3 /A GLY 44 HA2 -0.309 2.309 /A TYR 163 CE2 /A ARG 48 HD3 -0.312 3.012 /A GLU 150 CG /A GLN 154 HE22 -0.312 3.012 /A SER 145 O /A GLU 148 HB2 -0.312 2.792 /A ARG 153 HG2 /A LEU 19 HD11 -0.315 2.315 /A ASP 146 C /A GLU 150 H -0.318 3.018 /A ILE 160 HG22 /A ASP 21 OD1 -0.319 2.799 /A ALA 156 O /A PRO 157 O -0.319 3.279 /A GLU 148 CD /A PHE 26 CD2 -0.321 3.721 /A ALA 152 CB /A ILE 25 CG2 -0.324 3.724 /A ILE 149 HG13 /A SER 145 O -0.324 2.804 /A TRP 141 CZ3 /A VAL 144 HG22 -0.325 3.025 /A LYS 155 H /A ARG 153 C -0.326 3.026 /A GLU 148 HG3 /A SER 145 HG -0.327 2.327 /A GLU 150 H /A GLU 147 C -0.329 3.029 /A ARG 153 HG2 /A LEU 19 CD2 -0.330 3.030 /A THR 161 H /A ASP 21 HB2 -0.334 2.334 /A ALA 156 H /A GLN 154 C -0.334 3.034 /A ILE 149 O /A ARG 153 CD -0.334 3.514 /A LYS 155 NZ /A GLU 40 O -0.335 3.040 /A GLU 151 O /A LYS 155 N -0.336 3.041 /A VAL 144 HG11 /A PHE 26 HB3 -0.339 2.339 /A ALA 152 HB2 /A ILE 25 HA -0.339 2.339 /A ALA 152 O /A GLY 44 HA3 -0.346 2.826 /A LYS 155 O /A ALA 156 O -0.347 3.307 /A GLU 148 OE2 /A SER 145 OG -0.348 2.928 /A ILE 143 H /A VAL 144 H -0.349 2.349 /A GLU 147 O /A GLU 150 HB3 -0.350 2.830 /A ALA 156 CA /A GLY 44 O -0.353 3.533 /A ALA 152 HB3 /A ILE 25 HG21 -0.354 2.354 /A GLN 154 H /A GLU 151 C -0.356 3.056 /A LYS 155 C /A GLY 44 HA2 -0.359 3.059 /A ILE 160 O /A ARG 162 N -0.359 3.064 /A GLU 148 O /A ALA 152 HB1 -0.360 2.840 /A GLU 150 HA /A ARG 153 HB3 -0.362 2.362 /A ARG 153 HH21 /A ARG 18 NH2 -0.363 2.988 /A GLU 151 OE1 /A LYS 155 HE3 -0.363 2.843 /A GLU 148 CB /A SER 145 HG -0.367 3.067 /A TRP 141 HZ2 /A TYR 105 HE2 -0.368 2.368 /A GLU 159 H /A PRO 157 HB3 -0.370 2.370 /A ALA 152 O /A GLY 44 CA -0.370 3.550 /A TRP 141 CH2 /A TYR 105 CE1 -0.370 3.770 /A GLU 148 C /A ALA 152 H -0.373 3.073 /A ARG 153 H /A GLU 151 C -0.373 3.073 /A GLU 151 O /A LYS 155 CB -0.378 3.558 /A SER 145 OG /A GLU 148 N -0.381 3.106 /A LYS 155 NZ /A GLU 40 C -0.382 3.707 /A GLN 154 HE22 /A GLU 150 HG2 -0.384 2.384 /A ILE 149 C /A ARG 153 H -0.385 3.085 /A SER 145 C /A GLU 148 H -0.389 3.089 /A ILE 149 H /A GLU 147 C -0.389 3.089 /A ILE 149 HG12 /A ILE 25 CD1 -0.392 3.092 /A GLU 150 O /A GLU 151 O -0.393 3.353 /A ILE 149 CG1 /A SER 145 O -0.394 3.574 /A LYS 155 CB /A LEU 43 O -0.396 3.576 /A PRO 157 CG /A ASP 21 CB -0.398 3.798 /A ILE 143 N /A GLU 140 C -0.398 3.723 /A TRP 141 CE2 /A MET 96 CE -0.398 3.798 /A ILE 143 CG1 /A GLU 140 HA -0.399 3.099 220 contacts > select clear Alignment identifier is 1/A > select /A:138 15 atoms, 14 bonds, 1 residue, 1 model selected > select /A:138-141 69 atoms, 70 bonds, 4 residues, 1 model selected > select /A:137 16 atoms, 15 bonds, 1 residue, 1 model selected > select /A:137-141 85 atoms, 86 bonds, 5 residues, 1 model selected > select /A:140 15 atoms, 14 bonds, 1 residue, 1 model selected > select /A:140-141 39 atoms, 40 bonds, 2 residues, 1 model selected > ui tool show AlphaFold > alphafold predict > LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGVMLIKKTAENIDEAVEEEWVIVSDEEIEEARQKAPLEITRY Running AlphaFold prediction > close > open /Users/chenyang/Desktop/fbp1.cxs format session Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #3, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at level 1.5, step 1, values float32 Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #5, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at level 0.412, step 1, values float32 Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #6, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at level 0.208, step 1, values float32 opened ChimeraX session > hide #* target a > show #1,3-6 target ab > hide #4#!1 cartoons > close > open /Users/chenyang/Desktop/fbp1.cxs format session Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #3, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at level 1.5, step 1, values float32 Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #5, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at level 0.412, step 1, values float32 Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #6, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at level 0.208, step 1, values float32 opened ChimeraX session > close #4 > hide #!5 models > hide #!6 models > show #!6 models > show #!5 models > volume style mesh > show #!2 models > hide #!2 models > close > open ""/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine > 10/FBP1_R50A_refine_10.pdb"" Summary of feedback from opening /Users/chenyang/Desktop/FBP1_R50A_GGPP/refine 10/FBP1_R50A_refine_10.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2022-01-10 Time 22:38:17 CST +0800 (1641825497.80 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /media/Elements_/BL18/2022/caoyu/good/caolab001_13/cao/output.sca 42 messages similar to the above omitted Chain information for FBP1_R50A_refine_10.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > open ""/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine > 10/FBP1_R50A_refine_10_2mFo-DFc.ccp4"" Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #2, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at level 3.49, step 1, values float32 > volume #2 level 1.5 > volume style mesh > transparency 50 > volume showOutlineBox true > volume showOutlineBox false > volume step 2 > volume step 1 > volume step 2 > volume step 1 > vop gaussian #2 sdev 2.05 Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #3, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at step 1, values float32 > surface dust #3 size 6.84 > undo > close #3 > show #!2 models > fitmap #1 inMap #2 Fit molecule FBP1_R50A_refine_10.pdb (#1) to map FBP1_R50A_refine_10_2mFo- DFc.ccp4 (#2) using 9250 atoms average map value = 2.813, steps = 40 shifted from previous position = 0.00374 rotated from previous position = 0.00554 degrees atoms outside contour = 1097, contour level = 1.5 Position of FBP1_R50A_refine_10.pdb (#1) relative to FBP1_R50A_refine_10_2mFo- DFc.ccp4 (#2) coordinates: Matrix rotation and translation 1.00000000 -0.00001379 -0.00003225 0.00093168 0.00001379 1.00000000 -0.00009016 -0.00229194 0.00003225 0.00009016 1.00000000 -0.00586216 Axis 0.93196568 -0.33335243 0.14253467 Axis point 0.00000000 66.28018853 -22.47865262 Rotation angle (degrees) 0.00554272 Shift along axis 0.00079676 > fitmap #1 inMap #2 Fit molecule FBP1_R50A_refine_10.pdb (#1) to map FBP1_R50A_refine_10_2mFo- DFc.ccp4 (#2) using 9250 atoms average map value = 2.813, steps = 44 shifted from previous position = 0.00984 rotated from previous position = 0.0131 degrees atoms outside contour = 1100, contour level = 1.5 Position of FBP1_R50A_refine_10.pdb (#1) relative to FBP1_R50A_refine_10_2mFo- DFc.ccp4 (#2) coordinates: Matrix rotation and translation 1.00000000 -0.00000714 0.00003105 0.00073557 0.00000713 0.99999999 0.00012920 0.00374498 -0.00003105 -0.00012920 0.99999999 0.00637562 Axis -0.97092271 0.23330833 0.05363122 Axis point 0.00000000 49.14151613 -28.07758643 Rotation angle (degrees) 0.00762419 Shift along axis 0.00050148 > close #2 > open ""/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine > 10/FBP1_R50A_refine_10_2mFo-DFc.ccp4"" Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #2, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at level 3.49, step 1, values float32 > transparency 50 > volume style image > volume style mesh > volume #2 style image > volume #2 level 1.5,0 level 3.492,0.8 level 8.163,1 > volume #2 maximumIntensityProjection true > volume #2 region 0,0,81,127,187,81 step 1 maximumIntensityProjection false > showOutlineBox true > volume #2 region 0,0,0,127,187,162 step 1 > volume #2 style mesh region 0,0,0,127,187,162 step 1 > volume #2 level 1.5 > volume #2 color #00f900 > volume #2 color #fffb00 > volume #2 color #00fdff > hide cartoons > show atoms > ui tool show ""Color Zone"" Drag select of 1 bonds Drag select of 3 atoms, 2 bonds, 2 FBP1_R50A_refine_10_2mFo-DFc.ccp4 > select clear Drag select of 4 atoms, 4 bonds, 2 FBP1_R50A_refine_10_2mFo-DFc.ccp4 > select clear Drag select of 5 atoms, 5 bonds > color zone #2 near sel distance 4.08 > show #2.2 models > color zone #2 near sel distance 4.08 > color single #2 > color zone #2 near sel distance 4.08 > volume splitbyzone #2 Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 0 as #3.1, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at step 1, values float32 Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 1 as #3.2, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at step 1, values float32 Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 2 as #3.3, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at step 1, values float32 > color zone #2 near sel distance 4.08 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!3.1 models > show #!3.1 models > hide #!3.2 models > show #!3.2 models > help help:user/tools/colorzone.html > close > open /Users/chenyang/Desktop/fbp1.cxs format session Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #3, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at level 1.5, step 1, values float32 Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #5, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at level 0.412, step 1, values float32 Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 gaussian as #6, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at level 0.208, step 1, values float32 opened ChimeraX session > close > open 7cvh format mmcif fromDatabase pdb 7cvh title: Human Fructose-1,6-bisphosphatase 1 in complex with geranylgeranyl diphosphate [more info...] Chain information for 7cvh #1 --- Chain | Description | UniProt A B C D | Fructose-1,6-bisphosphatase 1 | F16P1_HUMAN Non-standard residues in 7cvh #1 --- AMP — adenosine monophosphate FBP — 1,6-di-O-phosphono-beta-D-fructofuranose (BETA-FRUCTOSE-1,6-DIPHOSPHATE; FRUCTOSE-1,6-BISPHOSPHATE; 1,6-di-O-phosphono-beta-D-fructose; 1,6-di-O- phosphono-D-fructose; 1,6-di-O-phosphono-fructose) GRG — geranylgeranyl diphosphate MG — magnesium ion > open ""/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine > 10/FBP1_R50A_refine_10_2mFo-DFc.ccp4"" Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #2, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at level 3.49, step 1, values float32 > open ""/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine > 10/FBP1_R50A_refine_10.pdb"" Summary of feedback from opening /Users/chenyang/Desktop/FBP1_R50A_GGPP/refine 10/FBP1_R50A_refine_10.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2022-01-10 Time 22:38:17 CST +0800 (1641825497.80 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /media/Elements_/BL18/2022/caoyu/good/caolab001_13/cao/output.sca 42 messages similar to the above omitted Chain information for FBP1_R50A_refine_10.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > hide #!1 models > volume style mesh > volume #2 level 1.5 > volume step 2 > transparency 50 > volume zone #2 nearAtoms #3 range 4.1 > undo Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic models, 1 maps. > hide #!1 models > volume zone #2 nearAtoms #3 range 4.1 > undo > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > close > open ""/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine > 10/FBP1_R50A_refine_10.pdb"" Summary of feedback from opening /Users/chenyang/Desktop/FBP1_R50A_GGPP/refine 10/FBP1_R50A_refine_10.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2022-01-10 Time 22:38:17 CST +0800 (1641825497.80 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /media/Elements_/BL18/2022/caoyu/good/caolab001_13/cao/output.sca 42 messages similar to the above omitted Chain information for FBP1_R50A_refine_10.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > open ""/Users/chenyang/Desktop/FBP1_R50A_GGPP/refine > 10/FBP1_R50A_refine_10_2mFo-DFc.ccp4"" Opened FBP1_R50A_refine_10_2mFo-DFc.ccp4 as #2, grid size 128,188,163, pixel 0.681,0.684,0.68, shown at level 3.49, step 1, values float32 > volume zone #2 nearAtoms #1 range 4.1 > undo > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > volume zone #2 nearAtoms #1 range 4.1 > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > volume style mesh > volume #2 level 2 > transparency 50 > ui tool show AlphaFold No sequence chosen for AlphaFold predict > help help:user/tools/alphafold.html No sequence chosen for AlphaFold search No sequence chosen for AlphaFold match > alphafold predict > LATTLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGVMLIKKTAENIDEAVEEEWVIVSDEEIEEARQKAPLEITRY Running AlphaFold prediction > ui tool show ""Volume Viewer"" > transparency 0 > transparency 50 > help help:user Chain information for best_model.pdb #3 --- Chain | Description A | No description available AlphaFold prediction finished Results in /Users/chenyang/Downloads/ChimeraX/AlphaFold/prediction_3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.1 OpenGL renderer: Apple M1 OpenGL vendor: AppleHardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache: 8 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 12.0.1 (21A559) Kernel Version: Darwin 21.1.0 Time since boot: 6 days 20:22 Graphics/Displays: Apple G13G: Chipset Model: Apple G13G Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect assigned normal UI Tom Goddard all ChimeraX