id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2584 bounds determination: zero-size array to reduction operation minimum which has no identity Elaine Meng Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-11-15) Description Got a traceback in the ""coordset"" playback from the ""morph"" command after going through most of this long tutorial: http://www.cgl.ucsf.edu/home/meng/chimera-tutorials/presentations/modules/chimerax-comp-structures/#/0/22 Haven't reproduced with a short series of actions. However, there seem to be no bad side effects of this traceback. Morph is created and plays back, slider is shown. Log: > open /Users/meng/Desktop/startup.cxc > alias reset view orient; view initial > alias start toolshed show $1 executed startup.cxc UCSF ChimeraX version: 0.91 (2019-11-15) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Unknown command: http://www.cgl.ucsf.edu/home/meng/chimera- tutorials/presentations/modules/chimerax-comp-structures/#/ > open http://www.cgl.ucsf.edu/home/meng/chimera- tutorials/presentations/modules/chimerax-comp-structures/#/ Opened 'http://www.cgl.ucsf.edu/home/meng/chimera- tutorials/presentations/modules/chimerax-comp-structures/#/' in browser > open http://www.cgl.ucsf.edu/home/meng/chimera- tutorials/presentations/modules/chimerax-comp-structures/#/ Opened 'http://www.cgl.ucsf.edu/home/meng/chimera- tutorials/presentations/modules/chimerax-comp-structures/#/' in browser > open /Users/meng/Desktop/chidata/test.stl Opened STL file containing 17094 triangles > close > toolshed show ""Side View"" > open 3w7f 3w7f title: Crystal structure of the C(30) carotenoid dehydrosqualene synthase from staphylococcus aureus complexed with farnesyl thiopyrophosphate [more info...] Chain information for 3w7f #1 --- Chain | Description A B | Dehydrosqualene synthase Non-standard residues in 3w7f #1 --- FPS — S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate (farnesyl thiopyrophosphate) MG — magnesium ion 3w7f mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > delete /b > label ligand > label height 1.0 Missing ""showPivot"" keyword's argument > cofr showPivot true > cofr showPivot false > delete solvent > label @@display > select /A:21@OG 1 atom, 1 model selected > distance /A:21@OG /A:302@O2B Distance between /A SER 21 OG and FPS 302 O2B: 3.332Å > select /A:21@OG 1 atom, 1 model selected > distance /A:21@OG /A:302@O1B Distance between /A SER 21 OG and FPS 302 O1B: 2.405Å > select /A:248@OH 1 atom, 1 model selected > distance /A:248@OH /A:302@O1B Distance between /A TYR 248 OH and FPS 302 O1B: 2.996Å > ~distance > select clear > distance :21@OG :302@O1B Distance between /A SER 21 OG and FPS 302 O1B: 2.405Å > distance :248@OH :302@O1B Distance between /A TYR 248 OH and FPS 302 O1B: 2.996Å > select :fps 48 atoms, 46 bonds, 1 model selected > select clear > select :FPS 48 atoms, 46 bonds, 1 model selected > select clear > select :FPS 48 atoms, 46 bonds, 1 model selected > hbonds sel restrict cross log true reveal true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 3w7f 13 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A SER 19 OG /A FPS 302 O2A no hydrogen 2.886 N/A /A SER 21 N /A FPS 302 O2B no hydrogen 3.185 N/A /A SER 21 OG /A FPS 302 O1B no hydrogen 2.405 N/A /A SER 21 OG /A FPS 302 O2B no hydrogen 3.332 N/A /A TYR 41 OH /A FPS 302 O2A no hydrogen 2.585 N/A /A ARG 45 NH1 /A FPS 301 O2B no hydrogen 3.428 N/A /A ARG 45 NH1 /A FPS 301 O3B no hydrogen 2.585 N/A /A ARG 45 NH2 /A FPS 301 O2B no hydrogen 3.175 N/A /A ARG 45 NH2 /A FPS 302 O1A no hydrogen 3.052 N/A /A ARG 171 NH1 /A FPS 302 O1B no hydrogen 2.685 N/A /A ARG 171 NH1 /A FPS 302 O3B no hydrogen 3.412 N/A /A ARG 171 NH2 /A FPS 302 O3B no hydrogen 3.129 N/A /A TYR 248 OH /A FPS 302 O1B no hydrogen 2.996 N/A 13 hydrogen bonds found > toolshed show H-Bonds > toolshed show H-Bonds > info path user unversioned config user unversioned config directory: /Users/meng/Library/Application Support/ChimeraX > toolshed show H-Bonds > hbonds sel restrict cross reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 3w7f 13 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A SER 19 OG /A FPS 302 O2A no hydrogen 2.886 N/A /A SER 21 N /A FPS 302 O2B no hydrogen 3.185 N/A /A SER 21 OG /A FPS 302 O1B no hydrogen 2.405 N/A /A SER 21 OG /A FPS 302 O2B no hydrogen 3.332 N/A /A TYR 41 OH /A FPS 302 O2A no hydrogen 2.585 N/A /A ARG 45 NH1 /A FPS 301 O2B no hydrogen 3.428 N/A /A ARG 45 NH1 /A FPS 301 O3B no hydrogen 2.585 N/A /A ARG 45 NH2 /A FPS 301 O2B no hydrogen 3.175 N/A /A ARG 45 NH2 /A FPS 302 O1A no hydrogen 3.052 N/A /A ARG 171 NH1 /A FPS 302 O1B no hydrogen 2.685 N/A /A ARG 171 NH1 /A FPS 302 O3B no hydrogen 3.412 N/A /A ARG 171 NH2 /A FPS 302 O3B no hydrogen 3.129 N/A /A TYR 248 OH /A FPS 302 O1B no hydrogen 2.996 N/A 13 hydrogen bonds found > hbonds sel restrict cross reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 3w7f 13 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A SER 19 OG /A FPS 302 O2A no hydrogen 2.886 N/A /A SER 21 N /A FPS 302 O2B no hydrogen 3.185 N/A /A SER 21 OG /A FPS 302 O1B no hydrogen 2.405 N/A /A SER 21 OG /A FPS 302 O2B no hydrogen 3.332 N/A /A TYR 41 OH /A FPS 302 O2A no hydrogen 2.585 N/A /A ARG 45 NH1 /A FPS 301 O2B no hydrogen 3.428 N/A /A ARG 45 NH1 /A FPS 301 O3B no hydrogen 2.585 N/A /A ARG 45 NH2 /A FPS 301 O2B no hydrogen 3.175 N/A /A ARG 45 NH2 /A FPS 302 O1A no hydrogen 3.052 N/A /A ARG 171 NH1 /A FPS 302 O1B no hydrogen 2.685 N/A /A ARG 171 NH1 /A FPS 302 O3B no hydrogen 3.412 N/A /A ARG 171 NH2 /A FPS 302 O3B no hydrogen 3.129 N/A /A TYR 248 OH /A FPS 302 O1B no hydrogen 2.996 N/A 13 hydrogen bonds found > ~hbonds > ~distance > contacts sel restrict cross reveal true log true select 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 86 contacts atom1 atom2 overlap distance /A FPS 301 C10 /A CYS 44 CB 0.472 3.288 /A FPS 302 O2A /A SER 19 CB 0.387 2.913 /A FPS 301 PB /A ARG 45 NH1 0.248 3.492 /A FPS 302 O2A /A SER 19 CA 0.242 3.058 /A FPS 302 O1B /A SER 21 CB 0.215 3.085 /A FPS 302 C14 /A ALA 157 CB 0.208 3.552 /A FPS 301 C7 /A CYS 44 CB 0.207 3.433 /A FPS 302 C14 /A ALA 157 CA 0.191 3.569 /A FPS 301 C6 /A ASP 48 CB 0.166 3.474 /A FPS 301 C15 /A TYR 41 CD2 0.158 3.482 /A FPS 301 O2A /A MG 303 MG 0.156 1.834 /A FPS 302 PB /A ARG 171 NH1 0.139 3.601 /A FPS 301 PA /A ASN 168 ND2 0.116 3.624 /A FPS 301 C14 /A LEU 141 CD1 0.106 3.654 /A FPS 302 O1A /A MG 304 MG 0.098 1.892 /A FPS 301 C8 /A CYS 44 CB 0.097 3.393 /A FPS 301 O2A /A ASN 168 OD1 0.097 2.743 /A FPS 301 O2A /A ASP 172 OD2 0.088 2.752 /A FPS 302 O1B /A SER 21 OG 0.075 2.405 /A FPS 301 O3B /A ARG 45 NH1 0.075 2.585 /A FPS 302 PB /A SER 21 OG 0.073 3.487 /A FPS 302 O3B /A MG 304 MG 0.039 1.951 /A FPS 301 C15 /A TYR 41 CE2 0.036 3.604 /A FPS 302 C4 /A GLN 165 OE1 -0.007 3.307 /A FPS 302 PA /A ARG 45 NH2 -0.011 3.751 /A FPS 301 C12 /A TYR 41 CD2 -0.015 3.535 /A FPS 302 PB /A SER 21 CB -0.023 4.003 /A FPS 302 O1B /A ARG 171 NH1 -0.025 2.685 /A FPS 302 C2 /A PHE 22 CE2 -0.038 3.558 /A FPS 301 C12 /A VAL 137 CG1 -0.048 3.688 /A FPS 301 O2B /A MG 304 MG -0.054 2.044 /A FPS 301 C2 /A ASP 48 CG -0.073 3.713 /A FPS 302 C10 /A GLY 161 CA -0.084 3.844 /A FPS 301 C11 /A TYR 41 CD2 -0.091 3.611 /A FPS 302 C5 /A ALA 134 CB -0.095 3.855 /A FPS 301 O1A /A MG 304 MG -0.097 2.087 /A FPS 301 O3B /A MG 305 MG -0.103 2.093 /A FPS 302 C5 /A LEU 164 CB -0.104 3.864 /A FPS 302 O2A /A TYR 41 OH -0.105 2.585 /A FPS 301 O3B /A ASP 48 OD2 -0.105 2.945 /A FPS 301 C13 /A TYR 41 CD2 -0.106 3.476 /A FPS 302 C15 /A LEU 145 CD1 -0.106 3.866 /A FPS 301 C11 /A TYR 41 CE2 -0.107 3.627 /A FPS 302 C12 /A LEU 160 CD2 -0.110 3.750 /A FPS 301 C9 /A ARG 45 NH2 -0.149 3.669 /A FPS 302 C11 /A LEU 164 CD1 -0.154 3.794 /A FPS 301 C5 /A ASP 48 CG -0.159 3.919 /A FPS 302 C1 /A PHE 22 CE2 -0.161 3.681 /A FPS 301 C9 /A TYR 41 CE2 -0.162 3.802 /A FPS 302 C1 /A TYR 248 OH -0.174 3.394 /A FPS 301 C9 /A ARG 45 CA -0.175 3.935 /A FPS 302 C4 /A ASN 168 CB -0.185 3.945 /A FPS 302 PB /A ARG 265 NH2 -0.191 3.931 /A FPS 302 C14 /A PHE 233 CZ -0.192 3.832 /A FPS 302 C4 /A ASN 168 ND2 -0.193 3.713 /A FPS 302 C15 /A LEU 141 CD1 -0.205 3.965 /A FPS 302 C4 /A GLN 165 CA -0.212 3.972 /A FPS 301 C15 /A MET 15 CE -0.215 3.975 /A FPS 302 PA /A SER 19 CB -0.217 4.197 /A FPS 302 O1B /A TYR 248 CE2 -0.227 3.407 /A FPS 302 C11 /A GLY 161 CA -0.230 3.870 /A FPS 302 C10 /A GLY 138 CA -0.231 3.991 /A FPS 302 PA /A SER 19 CA -0.232 4.212 /A FPS 302 C12 /A GLY 138 CA -0.237 3.877 /A FPS 302 PA /A SER 19 OG -0.239 3.799 /A FPS 301 C15 /A PHE 22 CD2 -0.249 3.889 /A FPS 301 C5 /A ASP 48 CB -0.250 4.010 /A FPS 301 PA /A ASN 168 OD1 -0.251 3.771 /A FPS 302 PA /A TYR 41 OH -0.259 3.819 /A FPS 302 C13 /A LEU 160 CD2 -0.264 3.754 /A FPS 302 C15 /A LEU 160 CD2 -0.279 4.039 /A FPS 301 C6 /A ASP 48 CG -0.284 3.924 /A FPS 301 C10 /A TYR 41 CD2 -0.296 3.936 /A FPS 301 C9 /A ARG 45 CZ -0.312 3.802 /A FPS 302 C10 /A LEU 141 CD1 -0.317 4.077 /A FPS 302 O2A /A TYR 41 CE2 -0.327 3.507 /A FPS 302 C7 /A ALA 134 CB -0.333 3.973 /A FPS 302 PB /A TYR 248 OH -0.356 3.916 /A FPS 302 C10 /A GLY 138 N -0.356 3.876 /A FPS 301 O2A /A ASN 168 CG -0.361 3.391 /A FPS 302 C7 /A GLY 161 CA -0.379 4.019 /A FPS 302 C14 /A PHE 233 CE1 -0.382 4.022 /A FPS 302 O2A /A HIS 18 O -0.390 3.230 /A FPS 302 C9 /A LEU 164 CD1 -0.390 4.150 /A FPS 302 O1A /A ARG 45 NH2 -0.392 3.052 /A FPS 302 C6 /A ALA 134 CB -0.396 4.036 86 contacts > ~select ligand 48 atoms, 1 model selected > ~select ions 45 atoms, 1 model selected > select :FPS 48 atoms, 46 bonds, 1 model selected > contacts sel restrict cross reveal true log true select 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 86 contacts atom1 atom2 overlap distance /A FPS 301 C10 /A CYS 44 CB 0.472 3.288 /A FPS 302 O2A /A SER 19 CB 0.387 2.913 /A FPS 301 PB /A ARG 45 NH1 0.248 3.492 /A FPS 302 O2A /A SER 19 CA 0.242 3.058 /A FPS 302 O1B /A SER 21 CB 0.215 3.085 /A FPS 302 C14 /A ALA 157 CB 0.208 3.552 /A FPS 301 C7 /A CYS 44 CB 0.207 3.433 /A FPS 302 C14 /A ALA 157 CA 0.191 3.569 /A FPS 301 C6 /A ASP 48 CB 0.166 3.474 /A FPS 301 C15 /A TYR 41 CD2 0.158 3.482 /A FPS 301 O2A /A MG 303 MG 0.156 1.834 /A FPS 302 PB /A ARG 171 NH1 0.139 3.601 /A FPS 301 PA /A ASN 168 ND2 0.116 3.624 /A FPS 301 C14 /A LEU 141 CD1 0.106 3.654 /A FPS 302 O1A /A MG 304 MG 0.098 1.892 /A FPS 301 C8 /A CYS 44 CB 0.097 3.393 /A FPS 301 O2A /A ASN 168 OD1 0.097 2.743 /A FPS 301 O2A /A ASP 172 OD2 0.088 2.752 /A FPS 302 O1B /A SER 21 OG 0.075 2.405 /A FPS 301 O3B /A ARG 45 NH1 0.075 2.585 /A FPS 302 PB /A SER 21 OG 0.073 3.487 /A FPS 302 O3B /A MG 304 MG 0.039 1.951 /A FPS 301 C15 /A TYR 41 CE2 0.036 3.604 /A FPS 302 C4 /A GLN 165 OE1 -0.007 3.307 /A FPS 302 PA /A ARG 45 NH2 -0.011 3.751 /A FPS 301 C12 /A TYR 41 CD2 -0.015 3.535 /A FPS 302 PB /A SER 21 CB -0.023 4.003 /A FPS 302 O1B /A ARG 171 NH1 -0.025 2.685 /A FPS 302 C2 /A PHE 22 CE2 -0.038 3.558 /A FPS 301 C12 /A VAL 137 CG1 -0.048 3.688 /A FPS 301 O2B /A MG 304 MG -0.054 2.044 /A FPS 301 C2 /A ASP 48 CG -0.073 3.713 /A FPS 302 C10 /A GLY 161 CA -0.084 3.844 /A FPS 301 C11 /A TYR 41 CD2 -0.091 3.611 /A FPS 302 C5 /A ALA 134 CB -0.095 3.855 /A FPS 301 O1A /A MG 304 MG -0.097 2.087 /A FPS 301 O3B /A MG 305 MG -0.103 2.093 /A FPS 302 C5 /A LEU 164 CB -0.104 3.864 /A FPS 302 O2A /A TYR 41 OH -0.105 2.585 /A FPS 301 O3B /A ASP 48 OD2 -0.105 2.945 /A FPS 301 C13 /A TYR 41 CD2 -0.106 3.476 /A FPS 302 C15 /A LEU 145 CD1 -0.106 3.866 /A FPS 301 C11 /A TYR 41 CE2 -0.107 3.627 /A FPS 302 C12 /A LEU 160 CD2 -0.110 3.750 /A FPS 301 C9 /A ARG 45 NH2 -0.149 3.669 /A FPS 302 C11 /A LEU 164 CD1 -0.154 3.794 /A FPS 301 C5 /A ASP 48 CG -0.159 3.919 /A FPS 302 C1 /A PHE 22 CE2 -0.161 3.681 /A FPS 301 C9 /A TYR 41 CE2 -0.162 3.802 /A FPS 302 C1 /A TYR 248 OH -0.174 3.394 /A FPS 301 C9 /A ARG 45 CA -0.175 3.935 /A FPS 302 C4 /A ASN 168 CB -0.185 3.945 /A FPS 302 PB /A ARG 265 NH2 -0.191 3.931 /A FPS 302 C14 /A PHE 233 CZ -0.192 3.832 /A FPS 302 C4 /A ASN 168 ND2 -0.193 3.713 /A FPS 302 C15 /A LEU 141 CD1 -0.205 3.965 /A FPS 302 C4 /A GLN 165 CA -0.212 3.972 /A FPS 301 C15 /A MET 15 CE -0.215 3.975 /A FPS 302 PA /A SER 19 CB -0.217 4.197 /A FPS 302 O1B /A TYR 248 CE2 -0.227 3.407 /A FPS 302 C11 /A GLY 161 CA -0.230 3.870 /A FPS 302 C10 /A GLY 138 CA -0.231 3.991 /A FPS 302 PA /A SER 19 CA -0.232 4.212 /A FPS 302 C12 /A GLY 138 CA -0.237 3.877 /A FPS 302 PA /A SER 19 OG -0.239 3.799 /A FPS 301 C15 /A PHE 22 CD2 -0.249 3.889 /A FPS 301 C5 /A ASP 48 CB -0.250 4.010 /A FPS 301 PA /A ASN 168 OD1 -0.251 3.771 /A FPS 302 PA /A TYR 41 OH -0.259 3.819 /A FPS 302 C13 /A LEU 160 CD2 -0.264 3.754 /A FPS 302 C15 /A LEU 160 CD2 -0.279 4.039 /A FPS 301 C6 /A ASP 48 CG -0.284 3.924 /A FPS 301 C10 /A TYR 41 CD2 -0.296 3.936 /A FPS 301 C9 /A ARG 45 CZ -0.312 3.802 /A FPS 302 C10 /A LEU 141 CD1 -0.317 4.077 /A FPS 302 O2A /A TYR 41 CE2 -0.327 3.507 /A FPS 302 C7 /A ALA 134 CB -0.333 3.973 /A FPS 302 PB /A TYR 248 OH -0.356 3.916 /A FPS 302 C10 /A GLY 138 N -0.356 3.876 /A FPS 301 O2A /A ASN 168 CG -0.361 3.391 /A FPS 302 C7 /A GLY 161 CA -0.379 4.019 /A FPS 302 C14 /A PHE 233 CE1 -0.382 4.022 /A FPS 302 O2A /A HIS 18 O -0.390 3.230 /A FPS 302 C9 /A LEU 164 CD1 -0.390 4.150 /A FPS 302 O1A /A ARG 45 NH2 -0.392 3.052 /A FPS 302 C6 /A ALA 134 CB -0.396 4.036 86 contacts > ~select :FPS 48 atoms, 1 model selected > ~select ions 45 atoms, 1 model selected > info residues sel residue id /A:15 name MET index 20 residue id /A:18 name HIS index 23 residue id /A:19 name SER index 24 residue id /A:21 name SER index 26 residue id /A:22 name PHE index 27 residue id /A:41 name TYR index 46 residue id /A:44 name CYS index 49 residue id /A:45 name ARG index 50 residue id /A:48 name ASP index 53 residue id /A:134 name ALA index 139 residue id /A:137 name VAL index 142 residue id /A:138 name GLY index 143 residue id /A:141 name LEU index 146 residue id /A:145 name LEU index 150 residue id /A:157 name ALA index 162 residue id /A:160 name LEU index 165 residue id /A:161 name GLY index 166 residue id /A:164 name LEU index 169 residue id /A:165 name GLN index 170 residue id /A:168 name ASN index 173 residue id /A:171 name ARG index 176 residue id /A:172 name ASP index 177 residue id /A:233 name PHE index 238 residue id /A:248 name TYR index 253 residue id /A:265 name ARG index 270 > select clear > label delete > contacts sel restrict cross reveal true log true select true No atoms in given atom specifier > select :FPS 48 atoms, 46 bonds, 1 model selected > contacts sel restrict cross reveal true log true select 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 86 contacts atom1 atom2 overlap distance /A FPS 301 C10 /A CYS 44 CB 0.472 3.288 /A FPS 302 O2A /A SER 19 CB 0.387 2.913 /A FPS 301 PB /A ARG 45 NH1 0.248 3.492 /A FPS 302 O2A /A SER 19 CA 0.242 3.058 /A FPS 302 O1B /A SER 21 CB 0.215 3.085 /A FPS 302 C14 /A ALA 157 CB 0.208 3.552 /A FPS 301 C7 /A CYS 44 CB 0.207 3.433 /A FPS 302 C14 /A ALA 157 CA 0.191 3.569 /A FPS 301 C6 /A ASP 48 CB 0.166 3.474 /A FPS 301 C15 /A TYR 41 CD2 0.158 3.482 /A FPS 301 O2A /A MG 303 MG 0.156 1.834 /A FPS 302 PB /A ARG 171 NH1 0.139 3.601 /A FPS 301 PA /A ASN 168 ND2 0.116 3.624 /A FPS 301 C14 /A LEU 141 CD1 0.106 3.654 /A FPS 302 O1A /A MG 304 MG 0.098 1.892 /A FPS 301 C8 /A CYS 44 CB 0.097 3.393 /A FPS 301 O2A /A ASN 168 OD1 0.097 2.743 /A FPS 301 O2A /A ASP 172 OD2 0.088 2.752 /A FPS 302 O1B /A SER 21 OG 0.075 2.405 /A FPS 301 O3B /A ARG 45 NH1 0.075 2.585 /A FPS 302 PB /A SER 21 OG 0.073 3.487 /A FPS 302 O3B /A MG 304 MG 0.039 1.951 /A FPS 301 C15 /A TYR 41 CE2 0.036 3.604 /A FPS 302 C4 /A GLN 165 OE1 -0.007 3.307 /A FPS 302 PA /A ARG 45 NH2 -0.011 3.751 /A FPS 301 C12 /A TYR 41 CD2 -0.015 3.535 /A FPS 302 PB /A SER 21 CB -0.023 4.003 /A FPS 302 O1B /A ARG 171 NH1 -0.025 2.685 /A FPS 302 C2 /A PHE 22 CE2 -0.038 3.558 /A FPS 301 C12 /A VAL 137 CG1 -0.048 3.688 /A FPS 301 O2B /A MG 304 MG -0.054 2.044 /A FPS 301 C2 /A ASP 48 CG -0.073 3.713 /A FPS 302 C10 /A GLY 161 CA -0.084 3.844 /A FPS 301 C11 /A TYR 41 CD2 -0.091 3.611 /A FPS 302 C5 /A ALA 134 CB -0.095 3.855 /A FPS 301 O1A /A MG 304 MG -0.097 2.087 /A FPS 301 O3B /A MG 305 MG -0.103 2.093 /A FPS 302 C5 /A LEU 164 CB -0.104 3.864 /A FPS 302 O2A /A TYR 41 OH -0.105 2.585 /A FPS 301 O3B /A ASP 48 OD2 -0.105 2.945 /A FPS 301 C13 /A TYR 41 CD2 -0.106 3.476 /A FPS 302 C15 /A LEU 145 CD1 -0.106 3.866 /A FPS 301 C11 /A TYR 41 CE2 -0.107 3.627 /A FPS 302 C12 /A LEU 160 CD2 -0.110 3.750 /A FPS 301 C9 /A ARG 45 NH2 -0.149 3.669 /A FPS 302 C11 /A LEU 164 CD1 -0.154 3.794 /A FPS 301 C5 /A ASP 48 CG -0.159 3.919 /A FPS 302 C1 /A PHE 22 CE2 -0.161 3.681 /A FPS 301 C9 /A TYR 41 CE2 -0.162 3.802 /A FPS 302 C1 /A TYR 248 OH -0.174 3.394 /A FPS 301 C9 /A ARG 45 CA -0.175 3.935 /A FPS 302 C4 /A ASN 168 CB -0.185 3.945 /A FPS 302 PB /A ARG 265 NH2 -0.191 3.931 /A FPS 302 C14 /A PHE 233 CZ -0.192 3.832 /A FPS 302 C4 /A ASN 168 ND2 -0.193 3.713 /A FPS 302 C15 /A LEU 141 CD1 -0.205 3.965 /A FPS 302 C4 /A GLN 165 CA -0.212 3.972 /A FPS 301 C15 /A MET 15 CE -0.215 3.975 /A FPS 302 PA /A SER 19 CB -0.217 4.197 /A FPS 302 O1B /A TYR 248 CE2 -0.227 3.407 /A FPS 302 C11 /A GLY 161 CA -0.230 3.870 /A FPS 302 C10 /A GLY 138 CA -0.231 3.991 /A FPS 302 PA /A SER 19 CA -0.232 4.212 /A FPS 302 C12 /A GLY 138 CA -0.237 3.877 /A FPS 302 PA /A SER 19 OG -0.239 3.799 /A FPS 301 C15 /A PHE 22 CD2 -0.249 3.889 /A FPS 301 C5 /A ASP 48 CB -0.250 4.010 /A FPS 301 PA /A ASN 168 OD1 -0.251 3.771 /A FPS 302 PA /A TYR 41 OH -0.259 3.819 /A FPS 302 C13 /A LEU 160 CD2 -0.264 3.754 /A FPS 302 C15 /A LEU 160 CD2 -0.279 4.039 /A FPS 301 C6 /A ASP 48 CG -0.284 3.924 /A FPS 301 C10 /A TYR 41 CD2 -0.296 3.936 /A FPS 301 C9 /A ARG 45 CZ -0.312 3.802 /A FPS 302 C10 /A LEU 141 CD1 -0.317 4.077 /A FPS 302 O2A /A TYR 41 CE2 -0.327 3.507 /A FPS 302 C7 /A ALA 134 CB -0.333 3.973 /A FPS 302 PB /A TYR 248 OH -0.356 3.916 /A FPS 302 C10 /A GLY 138 N -0.356 3.876 /A FPS 301 O2A /A ASN 168 CG -0.361 3.391 /A FPS 302 C7 /A GLY 161 CA -0.379 4.019 /A FPS 302 C14 /A PHE 233 CE1 -0.382 4.022 /A FPS 302 O2A /A HIS 18 O -0.390 3.230 /A FPS 302 C9 /A LEU 164 CD1 -0.390 4.150 /A FPS 302 O1A /A ARG 45 NH2 -0.392 3.052 /A FPS 302 C6 /A ALA 134 CB -0.396 4.036 86 contacts > ~select ~protein 45 atoms, 1 model selected > info residues sel residue id /A:15 name MET index 20 residue id /A:18 name HIS index 23 residue id /A:19 name SER index 24 residue id /A:21 name SER index 26 residue id /A:22 name PHE index 27 residue id /A:41 name TYR index 46 residue id /A:44 name CYS index 49 residue id /A:45 name ARG index 50 residue id /A:48 name ASP index 53 residue id /A:134 name ALA index 139 residue id /A:137 name VAL index 142 residue id /A:138 name GLY index 143 residue id /A:141 name LEU index 146 residue id /A:145 name LEU index 150 residue id /A:157 name ALA index 162 residue id /A:160 name LEU index 165 residue id /A:161 name GLY index 166 residue id /A:164 name LEU index 169 residue id /A:165 name GLN index 170 residue id /A:168 name ASN index 173 residue id /A:171 name ARG index 176 residue id /A:172 name ASP index 177 residue id /A:233 name PHE index 238 residue id /A:248 name TYR index 253 residue id /A:265 name ARG index 270 > ~contacts > select clear > label delete > label ligand > label height 1.0 > label @@display > select :FPS 48 atoms, 46 bonds, 1 model selected > hbonds sel restrict cross reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 3w7f 13 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A SER 19 OG /A FPS 302 O2A no hydrogen 2.886 N/A /A SER 21 N /A FPS 302 O2B no hydrogen 3.185 N/A /A SER 21 OG /A FPS 302 O1B no hydrogen 2.405 N/A /A SER 21 OG /A FPS 302 O2B no hydrogen 3.332 N/A /A TYR 41 OH /A FPS 302 O2A no hydrogen 2.585 N/A /A ARG 45 NH1 /A FPS 301 O2B no hydrogen 3.428 N/A /A ARG 45 NH1 /A FPS 301 O3B no hydrogen 2.585 N/A /A ARG 45 NH2 /A FPS 301 O2B no hydrogen 3.175 N/A /A ARG 45 NH2 /A FPS 302 O1A no hydrogen 3.052 N/A /A ARG 171 NH1 /A FPS 302 O1B no hydrogen 2.685 N/A /A ARG 171 NH1 /A FPS 302 O3B no hydrogen 3.412 N/A /A ARG 171 NH2 /A FPS 302 O3B no hydrogen 3.129 N/A /A TYR 248 OH /A FPS 302 O1B no hydrogen 2.996 N/A 13 hydrogen bonds found > toolshed show H-Bonds > ~hbonds > ~distance > distance :21@OG :302@O1B Distance between /A SER 21 OG and FPS 302 O1B: 2.405Å > distance :248@OH :302@O1B Distance between /A TYR 248 OH and FPS 302 O1B: 2.996Å > ~distance > contacts sel restrict cross reveal true log true select 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 86 contacts atom1 atom2 overlap distance /A FPS 301 C10 /A CYS 44 CB 0.472 3.288 /A FPS 302 O2A /A SER 19 CB 0.387 2.913 /A FPS 301 PB /A ARG 45 NH1 0.248 3.492 /A FPS 302 O2A /A SER 19 CA 0.242 3.058 /A FPS 302 O1B /A SER 21 CB 0.215 3.085 /A FPS 302 C14 /A ALA 157 CB 0.208 3.552 /A FPS 301 C7 /A CYS 44 CB 0.207 3.433 /A FPS 302 C14 /A ALA 157 CA 0.191 3.569 /A FPS 301 C6 /A ASP 48 CB 0.166 3.474 /A FPS 301 C15 /A TYR 41 CD2 0.158 3.482 /A FPS 301 O2A /A MG 303 MG 0.156 1.834 /A FPS 302 PB /A ARG 171 NH1 0.139 3.601 /A FPS 301 PA /A ASN 168 ND2 0.116 3.624 /A FPS 301 C14 /A LEU 141 CD1 0.106 3.654 /A FPS 302 O1A /A MG 304 MG 0.098 1.892 /A FPS 301 C8 /A CYS 44 CB 0.097 3.393 /A FPS 301 O2A /A ASN 168 OD1 0.097 2.743 /A FPS 301 O2A /A ASP 172 OD2 0.088 2.752 /A FPS 302 O1B /A SER 21 OG 0.075 2.405 /A FPS 301 O3B /A ARG 45 NH1 0.075 2.585 /A FPS 302 PB /A SER 21 OG 0.073 3.487 /A FPS 302 O3B /A MG 304 MG 0.039 1.951 /A FPS 301 C15 /A TYR 41 CE2 0.036 3.604 /A FPS 302 C4 /A GLN 165 OE1 -0.007 3.307 /A FPS 302 PA /A ARG 45 NH2 -0.011 3.751 /A FPS 301 C12 /A TYR 41 CD2 -0.015 3.535 /A FPS 302 PB /A SER 21 CB -0.023 4.003 /A FPS 302 O1B /A ARG 171 NH1 -0.025 2.685 /A FPS 302 C2 /A PHE 22 CE2 -0.038 3.558 /A FPS 301 C12 /A VAL 137 CG1 -0.048 3.688 /A FPS 301 O2B /A MG 304 MG -0.054 2.044 /A FPS 301 C2 /A ASP 48 CG -0.073 3.713 /A FPS 302 C10 /A GLY 161 CA -0.084 3.844 /A FPS 301 C11 /A TYR 41 CD2 -0.091 3.611 /A FPS 302 C5 /A ALA 134 CB -0.095 3.855 /A FPS 301 O1A /A MG 304 MG -0.097 2.087 /A FPS 301 O3B /A MG 305 MG -0.103 2.093 /A FPS 302 C5 /A LEU 164 CB -0.104 3.864 /A FPS 302 O2A /A TYR 41 OH -0.105 2.585 /A FPS 301 O3B /A ASP 48 OD2 -0.105 2.945 /A FPS 301 C13 /A TYR 41 CD2 -0.106 3.476 /A FPS 302 C15 /A LEU 145 CD1 -0.106 3.866 /A FPS 301 C11 /A TYR 41 CE2 -0.107 3.627 /A FPS 302 C12 /A LEU 160 CD2 -0.110 3.750 /A FPS 301 C9 /A ARG 45 NH2 -0.149 3.669 /A FPS 302 C11 /A LEU 164 CD1 -0.154 3.794 /A FPS 301 C5 /A ASP 48 CG -0.159 3.919 /A FPS 302 C1 /A PHE 22 CE2 -0.161 3.681 /A FPS 301 C9 /A TYR 41 CE2 -0.162 3.802 /A FPS 302 C1 /A TYR 248 OH -0.174 3.394 /A FPS 301 C9 /A ARG 45 CA -0.175 3.935 /A FPS 302 C4 /A ASN 168 CB -0.185 3.945 /A FPS 302 PB /A ARG 265 NH2 -0.191 3.931 /A FPS 302 C14 /A PHE 233 CZ -0.192 3.832 /A FPS 302 C4 /A ASN 168 ND2 -0.193 3.713 /A FPS 302 C15 /A LEU 141 CD1 -0.205 3.965 /A FPS 302 C4 /A GLN 165 CA -0.212 3.972 /A FPS 301 C15 /A MET 15 CE -0.215 3.975 /A FPS 302 PA /A SER 19 CB -0.217 4.197 /A FPS 302 O1B /A TYR 248 CE2 -0.227 3.407 /A FPS 302 C11 /A GLY 161 CA -0.230 3.870 /A FPS 302 C10 /A GLY 138 CA -0.231 3.991 /A FPS 302 PA /A SER 19 CA -0.232 4.212 /A FPS 302 C12 /A GLY 138 CA -0.237 3.877 /A FPS 302 PA /A SER 19 OG -0.239 3.799 /A FPS 301 C15 /A PHE 22 CD2 -0.249 3.889 /A FPS 301 C5 /A ASP 48 CB -0.250 4.010 /A FPS 301 PA /A ASN 168 OD1 -0.251 3.771 /A FPS 302 PA /A TYR 41 OH -0.259 3.819 /A FPS 302 C13 /A LEU 160 CD2 -0.264 3.754 /A FPS 302 C15 /A LEU 160 CD2 -0.279 4.039 /A FPS 301 C6 /A ASP 48 CG -0.284 3.924 /A FPS 301 C10 /A TYR 41 CD2 -0.296 3.936 /A FPS 301 C9 /A ARG 45 CZ -0.312 3.802 /A FPS 302 C10 /A LEU 141 CD1 -0.317 4.077 /A FPS 302 O2A /A TYR 41 CE2 -0.327 3.507 /A FPS 302 C7 /A ALA 134 CB -0.333 3.973 /A FPS 302 PB /A TYR 248 OH -0.356 3.916 /A FPS 302 C10 /A GLY 138 N -0.356 3.876 /A FPS 301 O2A /A ASN 168 CG -0.361 3.391 /A FPS 302 C7 /A GLY 161 CA -0.379 4.019 /A FPS 302 C14 /A PHE 233 CE1 -0.382 4.022 /A FPS 302 O2A /A HIS 18 O -0.390 3.230 /A FPS 302 C9 /A LEU 164 CD1 -0.390 4.150 /A FPS 302 O1A /A ARG 45 NH2 -0.392 3.052 /A FPS 302 C6 /A ALA 134 CB -0.396 4.036 86 contacts > ~select ~protein 45 atoms, 1 model selected > info residues sel residue id /A:15 name MET index 20 residue id /A:18 name HIS index 23 residue id /A:19 name SER index 24 residue id /A:21 name SER index 26 residue id /A:22 name PHE index 27 residue id /A:41 name TYR index 46 residue id /A:44 name CYS index 49 residue id /A:45 name ARG index 50 residue id /A:48 name ASP index 53 residue id /A:134 name ALA index 139 residue id /A:137 name VAL index 142 residue id /A:138 name GLY index 143 residue id /A:141 name LEU index 146 residue id /A:145 name LEU index 150 residue id /A:157 name ALA index 162 residue id /A:160 name LEU index 165 residue id /A:161 name GLY index 166 residue id /A:164 name LEU index 169 residue id /A:165 name GLN index 170 residue id /A:168 name ASN index 173 residue id /A:171 name ARG index 176 residue id /A:172 name ASP index 177 residue id /A:233 name PHE index 238 residue id /A:248 name TYR index 253 residue id /A:265 name ARG index 270 > ~contacts > select clear > label delete > mlp Map values for surface ""3w7f_A SES surface"": minimum -26.45, mean -3.954, maximum 24.82 > mlp Map values for surface ""3w7f_A SES surface"": minimum -26.45, mean -3.954, maximum 24.82 > ~ribbon > hide #1.2 models > ribbon > hide ribbons > ribbon > hide ribbons > hide protein > show #1.2 models > surface ligand @<6 visiblePatches 1 > surface ligand @<6.5 visiblePatches 1 Expected a keyword > surface ligand @<6.2 visiblePatches 1 > surface ligand @<6.3 visiblePatches 1 > surface ligand @<6.3 > mlp Map values for surface ""3w7f_A SES surface"": minimum -26.45, mean -3.954, maximum 24.82 > help surface zone > surface zone #1 nearAtoms ligand distance 5 > surface zone #1 nearAtoms ligand distance 4 > surface zone #1 nearAtoms ligand distance 5 maxComponents 1 > surface zone #1 nearAtoms ligand distance 6 maxComponents 1 Missing or invalid ""surfaces"" argument: empty atom specifier Expected a keyword > surface unzone #1 > surface zone #1 nearAtoms ligand distance 4 maxComponents 1 > surface unzone #1 > surface zone #1 nearAtoms ligand distance 5 maxComponents 1 > surface unzone #1 > surface zone #1 nearAtoms ligand distance 6 maxComponents 1 > surface zone #1 nearAtoms ligand distance 6 > surface unzone #1 > surface zone #1 nearAtoms ligand distance 4 > surface zone #1 nearAtoms ligand distance 5 > surface unzone #1 > hide ribbons > hide protein > surface ligand @<6.3 > show protein > show ribbons > preset ""initial styles"" ""original look"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > mlp Map values for surface ""3w7f_A SES surface"": minimum -26.45, mean -3.954, maximum 24.82 > surface ligand @<6.3 > hide ribbons > hide protein > preset sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" ""original look"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > mlp Map values for surface ""3w7f_A SES surface"": minimum -26.45, mean -3.954, maximum 24.82 > surface ligand @<6.3 > hide ribbons > hide protein > preset sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > style ligand sphere Changed 48 atom styles > preset ""initial styles"" sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > style ligand sphere Changed 48 atom styles > preset sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > style ligand sphere Changed 48 atom styles > color byattribute bfactor 2443 atoms, 289 residues, 1 surfaces, atom bfactor range 18.3 to 95.2 > color byattribute bfactor 2443 atoms, 289 residues, 1 surfaces, atom bfactor range 18.3 to 95.2 > open 2zco Summary of feedback from opening 2zco fetched from pdb --- note | Fetching compressed mmCIF 2zco from http://files.rcsb.org/download/2zco.cif 2zco title: Crystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus [more info...] Chain information for 2zco #2 --- Chain | Description A | Dehydrosqualene synthase > preset original Preset implemented in Python; no expansion to individual ChimeraX commands available. > mmaker #1 to #2 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2zco, chain A (#2) with 3w7f, chain A (#1), sequence alignment score = 1499.3 Alignment identifier is 1 RMSD between 277 pruned atom pairs is 0.608 angstroms; (across all 284 pairs: 0.886) > select ~sel 787 atoms, 160 bonds, 10 pseudobonds, 3 models selected > display sel & protein > ~select Nothing selected > select ~sel 787 atoms, 160 bonds, 10 pseudobonds, 3 models selected > label sel > label height 1.5 > label delete > select ~sel 787 atoms, 160 bonds, 10 pseudobonds, 3 models selected > display sel & protein > select ~sel 787 atoms, 160 bonds, 10 pseudobonds, 3 models selected > display sel & protein > select clear > morph #1,2 wrap true frames 60 hideModels true play true slider true Associated Morph - 3w7f chain A to 3w7f, chain A with 0 mismatches Computed 121 frame morph #3 > coordset #3 1,121 Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/sideview/tool.py"", line 116, in exposeEvent self.render() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/sideview/tool.py"", line 165, in render near, far = main_view.near_far_distances(main_camera, view_num) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 826, in near_far_distances near, far = self._near_far_bounds(cp, vd) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 839, in _near_far_bounds b = self.drawing_bounds(allow_drawing_changes = False) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 592, in drawing_bounds dm.cached_drawing_bounds = b = self.drawing.bounds() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 908, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 908, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 907, in bounds dbounds = [d.bounds() for d in self.child_drawings() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py"", line 908, in if d.display and not getattr(d, 'skip_bounds', False)] File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2125, in bounds xyz_min = amin([amin(c1 - r, axis=0), amin(c2 - r, axis=0)], axis=0) File ""<__array_function__ internals>"", line 6, in amin File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/numpy/core/fromnumeric.py"", line 2746, in amin keepdims=keepdims, initial=initial, where=where) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/numpy/core/fromnumeric.py"", line 90, in _wrapreduction return ufunc.reduce(obj, axis, dtype, out, **passkwargs) ValueError: zero-size array to reduction operation minimum which has no identity ValueError: zero-size array to reduction operation minimum which has no identity File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/numpy/core/fromnumeric.py"", line 90, in _wrapreduction return ufunc.reduce(obj, axis, dtype, out, **passkwargs) See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Graphics fixed all ChimeraX