id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1464 Addh on 1jj2: list index out of range lpravda@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-11-19) Description add hbond true. fails on Linux too. Log: UCSF ChimeraX version: 0.8 (2018-11-19) How to cite UCSF ChimeraX > open 1jj2 fromDatabase pdbe_updated 1jj2 title: Fully Refined Crystal Structure of the Haloarcula marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution [more info...] Chain information for 1jj2 #1 --- Chain | Description 0 | 23S ribosomal RNA 1 | ribosomal protein L39E 2 | ribosomal protein L44E 9 | 5S ribosomal RNA A | ribosomal protein L2 B | ribosomal protein L3 C | ribosomal protein L4 D | ribosomal protein L5 E | ribosomal protein L6 F | ribosomal protein L7AE G | ribosomal protein L10 H | ribosomal protein L10E I | ribosomal protein L13 J | ribosomal protein L14 K | ribosomal protein L15 L | ribosomal protein L15E M | ribosomal protein L18 N | ribosomal protein L18E O | ribosomal protein L19E P | ribosomal protein L21E Q | ribosomal protein L22 R | ribosomal protein L23 S | ribosomal protein L24 T | ribosomal protein L24E U | ribosomal protein L29 V | ribosomal protein L30 W | ribosomal protein L31E X | ribosomal protein L32E Y | RIBOSOMAL PROTEIN L37Ae Z | ribosomal protein L37E > addh hbond true Termini for 1jj2 (#1) chain 1 determined from SEQRES records Termini for 1jj2 (#1) chain O determined from SEQRES records Termini for 1jj2 (#1) chain P determined from SEQRES records Termini for 1jj2 (#1) chain F determined from SEQRES records Termini for 1jj2 (#1) chain Y determined from SEQRES records Termini for 1jj2 (#1) chain K determined from SEQRES records Termini for 1jj2 (#1) chain J determined from SEQRES records Termini for 1jj2 (#1) chain A determined from SEQRES records Termini for 1jj2 (#1) chain H determined from SEQRES records Termini for 1jj2 (#1) chain V determined from SEQRES records Termini for 1jj2 (#1) chain E determined from SEQRES records Termini for 1jj2 (#1) chain S determined from SEQRES records Termini for 1jj2 (#1) chain 9 determined from SEQRES records Termini for 1jj2 (#1) chain 2 determined from SEQRES records Termini for 1jj2 (#1) chain X determined from SEQRES records Termini for 1jj2 (#1) chain M determined from SEQRES records Termini for 1jj2 (#1) chain W determined from SEQRES records Termini for 1jj2 (#1) chain R determined from SEQRES records Termini for 1jj2 (#1) chain Q determined from SEQRES records Termini for 1jj2 (#1) chain 0 determined from SEQRES records Termini for 1jj2 (#1) chain U determined from SEQRES records Termini for 1jj2 (#1) chain Z determined from SEQRES records Termini for 1jj2 (#1) chain T determined from SEQRES records Termini for 1jj2 (#1) chain L determined from SEQRES records Termini for 1jj2 (#1) chain I determined from SEQRES records Termini for 1jj2 (#1) chain G determined from SEQRES records Termini for 1jj2 (#1) chain C determined from SEQRES records Termini for 1jj2 (#1) chain B determined from SEQRES records Termini for 1jj2 (#1) chain D determined from SEQRES records Termini for 1jj2 (#1) chain N determined from SEQRES records Chain-initial residues that are actual N termini: /1 GLY 1, /O THR 1, /P PRO 1, /F PRO 1, /Y ARG 10, /K THR 1, /J MET 1, /A GLY 1, /H LYS 1, /V MET 1, /E PRO 1, /S SER 1, /9 U 1, /2 MET 1, /M ALA 1, /R SER 1, /Q GLY 1, /U THR 1, /Z THR 1, /L ALA 1, /C MET 1, /B PRO 1, /N SER 1 Chain-initial residues that are not actual N termini: /1 ARG 35, /K PHE 89, /H ASP 109, /X THR 95, /W GLU 7, /0 U 10, /0 A 128, /0 G 716, /0 C 999, /0 U 1561, /0 U 1964, /0 G 2237, /0 G 2344, /0 G 2667, /T ARG 4, /I ALA 4, /G ILE 12, /G ARG 63, /D PHE 10, /D ALA 35, /D LEU 128 Chain-final residues that are actual C termini: /1 GLU 49, /P GLU 95, /F ARG 119, /Y ALA 82, /J VAL 132, /H ALA 167, /V ARG 154, /S ALA 119, /9 C 122, /2 GLU 92, /M LEU 186, /Z GLU 56, /L ALA 194, /I TRP 145, /C ARG 246, /B GLY 337, /N ARG 115 Chain-final residues that are not actual C termini: /1 GLU 31, /O ALA 143, /K GLU 83, /K GLN 150, /A GLY 237, /H LYS 97, /E PRO 172, /X VAL 236, /W GLU 88, /R ILE 81, /Q PRO 150, /0 U 125, /0 U 714, /0 U 970, /0 A 1559, /0 G 1951, /0 G 2136, /0 G 2338, /0 A 2664, /0 A 2914, /U ASP 65, /T ARG 56, /G SER 29, /G ASP 73, /D HIS 29, /D GLY 107, /D VAL 174 Missing OXT added to C-terminal residue /1 GLU 49 Missing OXT added to C-terminal residue /P GLU 95 Missing OXT added to C-terminal residue /F ARG 119 Missing OXT added to C-terminal residue /Y ALA 82 Missing OXT added to C-terminal residue /J VAL 132 Missing OXT added to C-terminal residue /H ALA 167 Missing OXT added to C-terminal residue /V ARG 154 Missing OXT added to C-terminal residue /S ALA 119 Missing OXT added to C-terminal residue /M LEU 186 Missing OXT added to C-terminal residue /Z GLU 56 Missing OXT added to C-terminal residue /L ALA 194 Missing OXT added to C-terminal residue /I TRP 145 Missing OXT added to C-terminal residue /C ARG 246 Missing OXT added to C-terminal residue /B GLY 337 Missing OXT added to C-terminal residue /N ARG 115 Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/cmd_line/tool.py"", line 225, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2581, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/cmd.py"", line 55, in cmd_addh add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/cmd.py"", line 163, in hbond_add_hydrogens idatm_type, his_Ns, coordinations, in_isolation) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/hbond.py"", line 241, in add_hydrogens hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop, angle_slop=rec_angle_slop) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/hbonds/hbond.py"", line 489, in find_hbonds limited_acceptors, generic_acc_info) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/hbonds/hbond.py"", line 749, in _find_acceptors acc_atom = group[acc_indices[i]] IndexError: list index out of range OpenGL version: 4.1 ATI-2.2.8 OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Structure Editing fixed all ChimeraX