id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1549 AddH: More than 2 coplanar positions specified! lpravda@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-12-17) Description open 3kch; addh Log: UCSF ChimeraX version: 0.8 (2018-12-17) How to cite UCSF ChimeraX > open 3kch 3kch title: Baranase crosslinked by glutaraldehyde [more info...] Chain information for 3kch #1 --- Chain | Description A B C | Ribonuclease Non-standard residues in 3kch #1 --- PTD — pentanedial 3kch mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly > addh Termini for 3kch (#1) chain A determined from SEQRES records Termini for 3kch (#1) chain C determined from SEQRES records Termini for 3kch (#1) chain B determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /A VAL 3, /C VAL 3, /B VAL 3 Chain-final residues that are actual C termini: /A ARG 110, /C ARG 110, /B ARG 110 Chain-final residues that are not actual C termini: Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/cmd_line/tool.py"", line 229, in execute cmd.run(cmd_text) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2587, in run result = ci.function(session, **kw_args) File ""/Users/chimera/Applications/ChimeraX_Daily.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 ""/Users/chimera/Applications/ChimeraX_Daily.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 ""/Users/chimera/Applications/ChimeraX_Daily.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 ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/hbonds/hbond.py"", line 568, in find_hbonds donor_hyds = hyd_positions(donor_atom) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/hbonds/hydpos.py"", line 77, in hyd_positions bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar)) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/bond_geom.py"", line 73, in bond_positions return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2, away2) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/bond_geom.py"", line 129, in planar_pos pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/bond_geom.py"", line 231, in angle_pos raise ValueError(""More than 2 coplanar positions specified!"") ValueError: More than 2 coplanar positions specified! ValueError: More than 2 coplanar positions specified! File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/atomic/bond_geom.py"", line 231, in angle_pos raise ValueError(""More than 2 coplanar positions specified!"") 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 Structure Editing fixed Elaine Meng all ChimeraX