id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1611 AddH: list index out of range in roomiest() lpravda@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-01-15) Description Structure protonation Log: UCSF ChimeraX version: 0.9 (2019-01-15) How to cite UCSF ChimeraX > open 1rju fromDatabase pdbe_updated Summary of feedback from opening 1rju fetched from pdbe_updated --- notes | Fetching compressed mmCIF 1rju from http://www.ebi.ac.uk/pdbe/entry- files/download/1rju_updated.cif Fetching CCD CU1 from http://ligand-expo.rcsb.org/reports/C/CU1/CU1.cif 1rju title: Crystal structure of a truncated form of yeast copper thionein [more info...] Chain information for 1rju #1 --- Chain | Description V | Metallothionein Non-standard residues in 1rju #1 --- CU1 — copper (I) ion > addh hbond true Summary of feedback from adding hydrogens to 1rju #1 --- notes | Termini for 1rju (#1) chain V determined from SEQRES records Chain-initial residues that are actual N termini: /V HIS 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /V ASN 36 Chain-final residues that are not actual C termini: 109 hydrogen bonds Traceback (most recent call last): File ""/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/cmd_line/tool.py"", line 252, in execute cmd.run(cmd_text) File ""/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2612, in run result = ci.function(session, **kw_args) File ""/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/cmd.py"", line 58, in cmd_addh add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes) File ""/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/cmd.py"", line 166, in hbond_add_hydrogens idatm_type, his_Ns, coordinations, in_isolation) File ""/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/hbond.py"", line 666, in add_hydrogens rooms = roomiest(remaining, a, _room_dist, bonding_info) File ""/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/cmd.py"", line 749, in roomiest return list(zip(*pos_info))[1] IndexError: list index out of range IndexError: list index out of range File ""/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/addh/cmd.py"", line 749, in roomiest return list(zip(*pos_info))[1] See log for complete Python traceback. OpenGL version: 4.1 ATI-2.4.9 OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Structure Editing fixed all ChimeraX