id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6215 Crash removing dock widget from main window 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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All rights reserved. How to cite UCSF ChimeraX > open /Users/Cailin/Desktop/agonist_1.pdb Chain information for agonist_1.pdb #1 --- Chain | Description B | No description available > hide #1.1 models > show #1.1 models > hide #1.1 models > hbonds reveal true 241 hydrogen bonds found Alignment identifier is 1/B > label #1.2#!1 atoms > label #1.2-3#!1 atoms attribute bfactor > hide #1.3 models Drag select of 1 residues > hide #1.2 models Drag select of 3 atoms, 6 bonds > select /B:285 6 atoms, 5 bonds, 1 residue, 1 model selected > select /B:4@CE2 1 atom, 1 residue, 1 model selected > select clear Drag select of 2 bonds > select clear > select /B:4@CE3 1 atom, 1 residue, 1 model selected Drag select of 1 residues, 1 bonds > select /B:285 6 atoms, 5 bonds, 1 residue, 1 model selected Drag select of 15 atoms, 4 residues, 14 bonds > select /B:449 10 atoms, 10 bonds, 1 residue, 1 model selected Drag select of 11 atoms, 2 residues, 14 bonds Drag select of 5 atoms, 7 bonds > select clear Drag select of 1 bonds Drag select of 2 bonds > select clear Drag select of 10 atoms, 1 residues, 13 bonds > ui mousemode right select > select clear Drag select of 3 atoms, 2 bonds > ui mousemode right select > preset ""molecular surfaces"" ""chain id coloring (opaque)"" Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color bychain targ s trans 0 > undo > hide #1.4 models > ~select #1.4 2 atoms, 2 bonds, 1 residue, 2 models selected > ui tool show ""Color Actions"" > color sel bypolymer > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select clear > interfaces ~solvent 0 buried areas: > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for agonist_1.pdb_B SES surface #1.4: minimum, -17.89, mean -1.45, maximum 12.60 To also show corresponding color key, enter the above coulombic command and add key true > transparency #1.4#!1 40 > transparency #1.4#!1 10 > transparency #1.4#!1 60 > interfaces ~solvent 0 buried areas: > hide #1.4 models > mlp Map values for surface ""agonist_1.pdb_B SES surface"": minimum -27.25, mean -3.469, maximum 22.53 To also show corresponding color key, enter the above mlp command and add key true > select /B:271@NE2 1 atom, 1 residue, 1 model selected > select /B:271@NE2 1 atom, 1 residue, 1 model selected > open /Users/Cailin/Desktop/agonist_2.pdb Chain information for agonist_2.pdb #2 --- Chain | Description A | No description available B | No description available > open /Users/Cailin/Desktop/antagonist.pdb Chain information for antagonist.pdb #3 --- Chain | Description A | No description available D | No description available > hide #!3 models > hide #1.4 models > hide #!1 models > select add #2/B:3@C12 2 atoms, 3 bonds, 2 residues, 3 models selected > select add #2/B:3@C15 3 atoms, 5 bonds, 2 residues, 3 models selected > select add #2/B:3@C10 4 atoms, 6 bonds, 2 residues, 3 models selected Drag select of 1 atoms Drag select of 2 atoms, 2 residues > select subtract #2/B:288 26 atoms, 24 bonds, 4 residues, 3 models selected > color (#!2 & sel) hot pink > undo > select subtract #2/B:368 15 atoms, 25 bonds, 3 residues, 3 models selected > select subtract #2/B:369 6 atoms, 24 bonds, 2 residues, 3 models selected > color (#!2 & sel) purple > select add #2/B:3@C4 1 atom, 2 bonds, 1 residue, 1 model selected > color sel purple > select #2/B:3@C17 1 atom, 1 residue, 1 model selected > color sel purple > undo > select #2/B:3@C11 1 atom, 1 residue, 1 model selected > select #2/B:3@C13 1 atom, 1 residue, 1 model selected > select #2/B:3@C14 1 atom, 1 residue, 1 model selected > select #2/B:3@C13 1 atom, 1 residue, 1 model selected > select add #2/B:3@C14 2 atoms, 7 bonds, 1 residue, 1 model selected > select add #2/B:3@C15 3 atoms, 7 bonds, 1 residue, 1 model selected > select add #2/B:3@C12 4 atoms, 7 bonds, 1 residue, 1 model selected > select add #2/B:3@C11 5 atoms, 7 bonds, 1 residue, 1 model selected Drag select of 1 atoms, 1 residues, 1 bonds > select subtract #2/A:350 6 atoms, 13 bonds, 1 residue, 1 model selected > color: sti & C salmon Unknown command: color: sti & C salmon Drag select of 1 atoms, 3 residues, 1 bonds > ui mousemode right translate Drag select of 1 atoms, 1 residues > ui mousemode right select > ui mousemode right rotate > ui mousemode right translate > select #2/B:259 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/B:259 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:352 11 atoms, 11 bonds, 1 residue, 1 model selected Drag select of 4 residues, 1 bonds > ui mousemode right translate > ui mousemode right rotate > ui mousemode right translate > ui mousemode right rotate > select clear > hbonds #!2 reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: agonist_2.pdb #2/A PRO 206 N; antagonist.pdb #3/A PRO 206 N; antagonist.pdb #3/D ARG 357 NE 2267 hydrogen bonds found Destroying pre-existing alignment with identifier 1/B Alignment identifier is 1/B Alignment identifier is 2/A Alignment identifier is 2/B Alignment identifier is 3/A Alignment identifier is 3/D > select #2/B:247-249,338-341,346-349 83 atoms, 82 bonds, 7 pseudobonds, 11 residues, 2 models selected > select > #2/B:208-225,230-238,252-263,277-302,306-308,311-333,350-354,360-362,365-377,381-392,403-424,431-457,467-472 1443 atoms, 1451 bonds, 161 pseudobonds, 179 residues, 2 models selected > select #3/A:247-249,338-341,346-349 83 atoms, 82 bonds, 11 residues, 1 model selected > select #3/D:449-475 152 atoms, 153 bonds, 1 pseudobond, 22 residues, 2 models selected > select #3/D:449-475 152 atoms, 153 bonds, 1 pseudobond, 22 residues, 2 models selected > color #!2 bynucleotide > label #2,4 text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > undo > label #2,4 attribute name Drag select of 5 residues, 1 bonds > ui mousemode right select > ui mousemode right rotate > ~label sel residues > hide #2.2 models > show #2.2 models > hide #2.2 models > show #2.2 models > hide #2.2 models > show #2.2 models > hide #2.2 models > hide (sel-residues & (protein|nucleic)) target ab > cartoon hide sel-residues > show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > undo > hide #3.1 models > style sel stick Changed 43 atom styles > label sel attribute label_specifier No visible Surface models selected > ui mousemode right select > select #2/B:3@C11 1 atom, 1 residue, 1 model selected > select clear > ui mousemode right select > ui mousemode right rotate > show (#4#2.1#!2 & sidechain) target ab > coulombic #!2 The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: agonist_2.pdb #2/A GLN 203 agonist_2.pdb #2/A LEU 204 agonist_2.pdb #2/A ASN 205 agonist_2.pdb #2/A PRO 206 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for agonist_2.pdb_A SES surface #2.4: minimum, -18.03, mean -2.09, maximum 13.21 Coulombic values for agonist_2.pdb_B SES surface #2.5: minimum, -20.97, mean -1.16, maximum 11.06 To also show corresponding color key, enter the above coulombic command and add key true > hide #2.3 models > show #2.3 models > hide #2.5 models > show #2.5 models > hide #2.4 models > show #2.4 models > hide #2.4 models > hide #2.3 models > show #2.3 models > hide #2.5 models > hide #!2 models > show #!3 models > coulombic #!3 The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: antagonist.pdb #3/A ASN 205 antagonist.pdb #3/A PRO 206 antagonist.pdb #3/A GLU 207 antagonist.pdb #3/A THR 242 antagonist.pdb #3/A GLU 259 antagonist.pdb #3/A ILE 262 antagonist.pdb #3/A LYS 263 antagonist.pdb #3/A SER 274 antagonist.pdb #3/A LYS 275 antagonist.pdb #3/A GLN 283 antagonist.pdb #3/A LYS 358 antagonist.pdb #3/A SER 428 antagonist.pdb #3/A GLN 430 antagonist.pdb #3/A LYS 434 antagonist.pdb #3/A GLN 444 antagonist.pdb #3/A LEU 452 antagonist.pdb #3/A LYS 474 antagonist.pdb #3/D SER 208 antagonist.pdb #3/D ARG 212 antagonist.pdb #3/D LYS 240 antagonist.pdb #3/D THR 242 antagonist.pdb #3/D LYS 263 antagonist.pdb #3/D THR 268 antagonist.pdb #3/D LYS 275 antagonist.pdb #3/D VAL 277 antagonist.pdb #3/D ARG 357 antagonist.pdb #3/D LYS 358 antagonist.pdb #3/D LYS 422 antagonist.pdb #3/D GLU 427 antagonist.pdb #3/D SER 429 antagonist.pdb #3/D GLN 430 antagonist.pdb #3/D THR 447 antagonist.pdb #3/D GLU 448 antagonist.pdb #3/D GLN 451 antagonist.pdb #3/D LEU 452 antagonist.pdb #3/D VAL 455 antagonist.pdb #3/D LYS 457 antagonist.pdb #3/D LYS 458 antagonist.pdb #3/D GLU 460 antagonist.pdb #3/D HIS 466 antagonist.pdb #3/D GLN 470 antagonist.pdb #3/D LYS 474 antagonist.pdb #3/D ASP 475 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HIS (net charge -4) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/k9/52yp04c17k11ykf6bljvnrd40000gn/T/tmp_sjlghjp/ante.in.mol2 -fi mol2 -o /var/folders/k9/52yp04c17k11ykf6bljvnrd40000gn/T/tmp_sjlghjp/ante.out.mol2 -fo mol2 -c bcc -nc -4 -j 5 -s 2 -dr n (HIS) `` (HIS) `Welcome to antechamber 20.0: molecular input file processor.` (HIS) `` (HIS) `Info: Finished reading file (/var/folders/k9/52yp04c17k11ykf6bljvnrd40000gn/T/tmp_sjlghjp/ante.in.mol2); atoms read (16), bonds read (15).` (HIS) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HIS) `Running: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HIS) `` (HIS) `` (HIS) `Running: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HIS) `Info: Total number of electrons: 64; net charge: -4` (HIS) `` (HIS) `Running: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HIS) `/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/antechamber: Fatal Error!` (HIS) `Cannot properly run ""/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out"".` Failure running ANTECHAMBER for residue HIS Check reply log for details > ui mousemode right select Drag select of 1 atoms, 1 residues > select #3/D:340 8 atoms, 7 bonds, 1 residue, 1 model selected > select subtract #3/D:340 1 bond, 1 model selected > select add #3/D:501@C05 1 atom, 2 bonds, 1 residue, 1 model selected > select subtract #3/D:501@C05 2 bonds, 1 model selected > select add #3/D:501@C08 1 atom, 5 bonds, 1 residue, 1 model selected > select add #3/D:501@C02 2 atoms, 9 bonds, 1 residue, 1 model selected > select add #3/D:501@C03 3 atoms, 9 bonds, 1 residue, 1 model selected > select add #3/D:501@C33 4 atoms, 17 bonds, 1 residue, 1 model selected > select add #3/D:501@C34 5 atoms, 18 bonds, 1 residue, 1 model selected > color sel red > undo > color sel lime > select add #3/D:501@C20 6 atoms, 22 bonds, 1 residue, 1 model selected > select add #3/D:501@C24 7 atoms, 22 bonds, 1 residue, 1 model selected > select add #3/D:501@C22 8 atoms, 23 bonds, 1 residue, 1 model selected > select add #3/D:501@C23 9 atoms, 24 bonds, 1 residue, 1 model selected > color (#!3 & sel) cyan > select add #3/D:501@C19 10 atoms, 33 bonds, 2 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C05 11 atoms, 35 bonds, 2 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C04 12 atoms, 35 bonds, 2 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > select add #3/D:501@C26 13 atoms, 36 bonds, 2 pseudobonds, 1 residue, 2 models selected > select subtract #3/D:501@C26 12 atoms, 36 bonds, 2 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C27 13 atoms, 36 bonds, 2 pseudobonds, 1 residue, 2 models selected > select add #3/D:281 21 atoms, 43 bonds, 2 pseudobonds, 2 residues, 2 models selected > select subtract #3/D:281@CG2 20 atoms, 41 bonds, 3 pseudobonds, 2 residues, 2 models selected > select subtract #3/D:281@CG1 19 atoms, 39 bonds, 3 pseudobonds, 2 residues, 2 models selected > select subtract #3/D:281@CB 18 atoms, 39 bonds, 3 pseudobonds, 2 residues, 2 models selected > select subtract #3/D:281 13 atoms, 36 bonds, 4 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C25 14 atoms, 37 bonds, 4 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C13 15 atoms, 37 bonds, 4 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > select add #3/D:501@C12 16 atoms, 37 bonds, 4 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > select add #3/D:501@C26 17 atoms, 37 bonds, 4 pseudobonds, 1 residue, 2 models selected > select subtract #3/D:501@C26 16 atoms, 37 bonds, 4 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C01 17 atoms, 38 bonds, 4 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > select add #3/D:501@C06 18 atoms, 38 bonds, 4 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C10 19 atoms, 38 bonds, 4 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > select add #3/D:501@C09 20 atoms, 39 bonds, 4 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > select add #3/D:501@C11 21 atoms, 39 bonds, 4 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C14 22 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > select add #3/D:501@C21 23 atoms, 39 bonds, 4 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > select add #3/D:501@C17 24 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C18 25 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C31 26 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected > select subtract #3/D:501@C31 25 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C32 26 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > select add #3/D:501@C31 27 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C35 28 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected > select subtract #3/D:501@C35 27 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > select add #3/D:501@C35 28 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > select add #3/D:501@C26 29 atoms, 41 bonds, 4 pseudobonds, 1 residue, 2 models selected > select subtract #3/D:501@C25 28 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C25 29 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C39 30 atoms, 39 bonds, 4 pseudobonds, 1 residue, 2 models selected > select subtract #3/D:501@C39 29 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C28 30 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected > select add #3/D:501@C29 31 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > select add #3/D:501@C30 32 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > select add #3/D:501@C39 33 atoms, 40 bonds, 4 pseudobonds, 1 residue, 2 models selected > color (#!3 & sel) cyan > hide #4 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > select clear > select add #2/B:3@C13 1 atom, 1 bond, 1 residue, 1 model selected > select add #2/B:3@C14 2 atoms, 3 bonds, 1 residue, 1 model selected > color sel purple > select add #2/B:3@C11 3 atoms, 5 bonds, 1 residue, 1 model selected > select add #2/B:3@C9 4 atoms, 6 bonds, 1 residue, 1 model selected > color sel purple > select add #2/B:3@C8 5 atoms, 9 bonds, 1 residue, 1 model selected > select add #2/B:3@C16 6 atoms, 10 bonds, 1 residue, 1 model selected > select add #2/B:3@C7 7 atoms, 12 bonds, 1 residue, 1 model selected > select add #2/B:3@C17 8 atoms, 13 bonds, 1 residue, 1 model selected > select add #2/B:3@C18 9 atoms, 14 bonds, 1 residue, 1 model selected > select add #2/B:3@C2 10 atoms, 20 bonds, 1 residue, 1 model selected > select add #2/B:3@C5 11 atoms, 21 bonds, 1 residue, 1 model selected > select add #2/B:442 19 atoms, 29 bonds, 2 residues, 1 model selected > select subtract #2/B:442 11 atoms, 22 bonds, 1 residue, 1 model selected > color sel purple > select add #2/B:3@C1 12 atoms, 22 bonds, 1 residue, 1 model selected > select subtract #2/B:3@C1 11 atoms, 22 bonds, 1 residue, 1 model selected > color sel purple > select add #2/B:3@C4 12 atoms, 24 bonds, 1 residue, 1 model selected > select add #2/B:3@C1 13 atoms, 24 bonds, 1 residue, 1 model selected > select add #2/B:3@C6 14 atoms, 25 bonds, 1 residue, 1 model selected > color sel purple > select add #2/B:3@C3 15 atoms, 25 bonds, 1 residue, 1 model selected > select subtract #2/B:3@C3 14 atoms, 25 bonds, 1 residue, 1 model selected > color sel purple > select add #2/B:3@C3 15 atoms, 25 bonds, 1 residue, 1 model selected > select subtract #2/B:3@C3 14 atoms, 25 bonds, 1 residue, 1 model selected > select add #2/B:3@C3 15 atoms, 25 bonds, 1 residue, 1 model selected > select subtract #2/B:3@C3 14 atoms, 25 bonds, 1 residue, 1 model selected > color sel purple > select subtract #2/B:3@C2 13 atoms, 25 bonds, 1 residue, 1 model selected > select add #2/B:3@C2 14 atoms, 25 bonds, 1 residue, 1 model selected > select subtract #2/B:3@C4 13 atoms, 25 bonds, 1 residue, 1 model selected > select add #2/B:3@C4 14 atoms, 25 bonds, 1 residue, 1 model selected > select add #2/B:3@C3 15 atoms, 25 bonds, 1 residue, 1 model selected > color sel purple > select ~sel 10599 atoms, 10498 bonds, 2280 pseudobonds, 1563 residues, 10 models selected > select subtract #2/B:3@N 10598 atoms, 10498 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:3@C 10597 atoms, 10497 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:3@C10 10596 atoms, 10496 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:3@C15 10595 atoms, 10496 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:3@C12 10594 atoms, 10496 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select add #2/B:3@C12 10595 atoms, 10496 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:3@C12 10594 atoms, 10496 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:3@CL 10593 atoms, 10497 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select add #2/B:3@C12 10594 atoms, 10500 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:441 10586 atoms, 10493 bonds, 2280 pseudobonds, 1562 residues, 13 models selected > select add #2/B:441 10594 atoms, 10500 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select add #2/B:3@C11 10595 atoms, 10501 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select add #2/B:3@C14 10596 atoms, 10503 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select add #2/B:3@C15 10597 atoms, 10503 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:3@C15 10596 atoms, 10503 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select add #2/B:3@C15 10597 atoms, 10503 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:3@O1 10596 atoms, 10504 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select add #2/B:3@C8 10597 atoms, 10511 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select add #2/B:3@C16 10598 atoms, 10514 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:3@O3 10597 atoms, 10515 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select add #2/B:3@C18 10598 atoms, 10515 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:3@C18 10597 atoms, 10516 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select add #2/B:3@C6 10598 atoms, 10515 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:3@C6 10597 atoms, 10515 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select add #2/B:3@C18 10598 atoms, 10516 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:3@C18 10597 atoms, 10516 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select add #2/B:3@C18 10598 atoms, 10516 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > select subtract #2/B:3@C18 10597 atoms, 10516 bonds, 2280 pseudobonds, 1563 residues, 13 models selected > color (#!2 & sel) orange > undo > ui mousemode right select > ui mousemode right rotate > ui mousemode right select > select #2/B:287 11 atoms, 11 bonds, 1 residue, 1 model selected > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > select add #1/B:4@CD2 1 atom, 2 bonds, 1 pseudobond, 1 residue, 2 models selected > select add #1/B:4@CG 2 atoms, 3 bonds, 1 pseudobond, 1 residue, 2 models selected > select add #1/B:4@CD1 3 atoms, 4 bonds, 1 pseudobond, 1 residue, 2 models selected > select add #1/B:4@CE2 4 atoms, 6 bonds, 1 pseudobond, 1 residue, 2 models selected > select add #1/B:4@CZ2 5 atoms, 7 bonds, 1 pseudobond, 1 residue, 2 models selected > select add #1/B:4@CZ3 6 atoms, 9 bonds, 1 pseudobond, 1 residue, 2 models selected > select add #1/B:4@CE3 7 atoms, 11 bonds, 1 pseudobond, 1 residue, 2 models selected > select add #1/B:4@CB 8 atoms, 11 bonds, 1 pseudobond, 1 residue, 2 models selected > select add #1/B:4@CA 9 atoms, 11 bonds, 1 pseudobond, 1 residue, 2 models selected > color (#!1 & sel) yellow > select add #1/B:4@CH2 10 atoms, 14 bonds, 1 pseudobond, 1 residue, 2 models selected > color (#!1 & sel) forest green > hbonds sel reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: agonist_2.pdb #2/A PRO 206 N; antagonist.pdb #3/A PRO 206 N; antagonist.pdb #3/D ARG 357 NE 0 hydrogen bonds found > select ligand 170 atoms, 185 bonds, 6 residues, 3 models selected > hbonds sel & #!1 reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: agonist_2.pdb #2/A PRO 206 N; antagonist.pdb #3/A PRO 206 N; antagonist.pdb #3/D ARG 357 NE 7 hydrogen bonds found > coulombic sel & #!1 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue SRO (net charge +1) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/k9/52yp04c17k11ykf6bljvnrd40000gn/T/tmp7alnnijr/ante.in.mol2 -fi mol2 -o /var/folders/k9/52yp04c17k11ykf6bljvnrd40000gn/T/tmp7alnnijr/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (SRO) `` (SRO) `Welcome to antechamber 20.0: molecular input file processor.` (SRO) `` (SRO) `Info: Finished reading file (/var/folders/k9/52yp04c17k11ykf6bljvnrd40000gn/T/tmp7alnnijr/ante.in.mol2); atoms read (26), bonds read (27).` (SRO) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (SRO) `Running: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (SRO) `` (SRO) `` (SRO) `Running: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (SRO) `Info: Total number of electrons: 94; net charge: 1` (SRO) `` (SRO) `Running: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (SRO) `` (SRO) `Running: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.3.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (SRO) `` (SRO) `Running: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (SRO) `` Charges for residue SRO determined Coulombic values for agonist_1.pdb_B SES surface #1.2: minimum, 1.12, mean 3.76, maximum 7.69 To also show corresponding color key, enter the above coulombic command and add key true Drag select of agonist_1.pdb_B SES surface, 5 of 3174 triangles > coulombic #!1 Coulombic values for agonist_1.pdb_B SES surface #1.4: minimum, -17.89, mean -1.45, maximum 12.60 To also show corresponding color key, enter the above coulombic command and add key true > coulombic #!1 Coulombic values for agonist_1.pdb_B SES surface #1.4: minimum, -17.89, mean -1.45, maximum 12.60 To also show corresponding color key, enter the above coulombic command and add key true > hide #1.4 models > hide #1.2 models No visible Surface models > show (#!1 & sidechain) target ab > hide #* target a > show #!1 target ab > hide #!1 models > show #!1 models > show #2.4 models > hide #2.4 models > show #2.4 models > hide #2.4 models > show #2.4 models > hide #2.4 models > show #!3 models > show #2.5 models > hide #2.5 models > hide #!1 models > hide #!2 models > select clear > show #!1 models > hide #2.1 models > hide #!3 models > select clear > select ligand 170 atoms, 185 bonds, 6 residues, 3 models selected > undo Drag select of 2 residues > select #1/B:230 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show Contacts > contacts select true color #992e1c reveal true 98337 contacts > contacts select true color #992e1c reveal true 98337 contacts > contacts select true color #992e1c reveal true 98337 contacts ===== 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 INTEL-18.3.5 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir7,2 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1.8 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 428.60.3.0.0 OS Loader Version: 540.60.2~89 SMC Version (system): 2.27f2 Software: System Software Overview: System Version: macOS 12.1 (21C52) Kernel Version: Darwin 21.2.0 Time since boot: 2 days 23:59 Graphics/Displays: Intel HD Graphics 6000: Chipset Model: Intel HD Graphics 6000 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1626 Revision ID: 0x0009 Metal Family: Supported, Metal GPUFamily macOS 1 Displays: Color LCD: Display Type: LCD Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus) UI Looks like: 1440 x 900 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes 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 closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX