id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2717 AddH: can't form new hydrogen name mpurdy@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-52-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.91 (2019-12-23) Description command line: addh hbond true or ISOLDE 1.0b4 add hydrogens Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /srv/cluster/NCEF/px/20190121_fPx1/2020-mp/build/RosCM_16_0006_KW01_pymol.pdb Chain information for RosCM_16_0006_KW01_pymol.pdb #1 --- Chain | Description A | No description available > addh hbond true Summary of feedback from adding hydrogens to RosCM_16_0006_KW01_pymol.pdb #1 --- notes | No usable SEQRES records for RosCM_16_0006_KW01_pymol.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLY 27 Chain-initial residues that are not actual N termini: /A GLN 63, /A VAL 101, /A PRO 196, /A LEU 211, /A ALA 260, /A LEU 314, /A LEU 332 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A THR 374, /A GLU 57, /A GLN 90, /A ALA 159, /A SER 208, /A ARG 251, /A PHE 301, /A LYS 325 197 hydrogen bonds Traceback (most recent call last): File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 62, in cmd_addh add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 170, in hbond_add_hydrogens idatm_type, his_Ns, coordinations, in_isolation) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/hbond.py"", line 747, in add_hydrogens _attach_hydrogens(a, altloc_hpos_info, bonding_info) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/hbond.py"", line 892, in _attach_hydrogens add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens, naming_schema) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 875, in add_altloc_hyds pos, bonding_info, alt_loc) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 901, in new_hydrogen new_h = add_atom(_h_name(parent_atom, h_num, total_hydrogens, naming_schema), ""H"", File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 1023, in _h_name while find_atom(""%s%s"" % (h_name, to_h36(h_num, h_digits))): File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 963, in to_h36 decimal_limit = eval('9' * max_digits) File """", line 0 ^ SyntaxError: unexpected EOF while parsing File """", line 0 ^ SyntaxError: unexpected EOF while parsing File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 963, in to_h36 decimal_limit = eval('9' * max_digits) See log for complete Python traceback. Downloading bundle ChimeraX_ISOLDE-1.0b4-cp37-cp37m-linux_x86_64.whl Successfully installed ChimeraX-Clipper-0.10.0 ChimeraX-ISOLDE-1.0b4 Installed ChimeraX-Clipper (0.10.0) Installed ChimeraX-ISOLDE (1.0b4) > toolshed show ISOLDE > set selectionWidth 4 Chain information for RosCM_16_0006_KW01_pymol.pdb --- Chain | Description 1.1/A | No description available Cached rota8000-val data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-leu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ile data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-pro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-phe data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-tyr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-trp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ser data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-thr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-cys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-met data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-lys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-his data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-arg data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asn data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-gln data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-glu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-cispro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-transpro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-gly-sym data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-prepro-noGP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-ileval-nopreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-general-noGPIVpreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Forcefield cache not found or out of date. Regenerating from ffXML files. This is normal if running ISOLDE for the first time, or after upgrading OpenMM. Done loading forcefield > open > /srv/cluster/NCEF/px/20190121_fPx1/2020-mp/build/csparc_P16_J45_1prot.mrc Opened csparc_P16_J45_1prot.mrc, grid size 256,256,256, pixel 1.06, shown at level 0.000125, step 1, values float32 No template found for residue A66 (CYS) Adding hydrogens Summary of feedback from adding hydrogens to RosCM_16_0006_KW01_pymol.pdb #1.1 --- notes | No usable SEQRES records for RosCM_16_0006_KW01_pymol.pdb (#1.1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A GLY 27 Chain-initial residues that are not actual N termini: /A GLN 63, /A VAL 101, /A PRO 196, /A LEU 211, /A ALA 260, /A LEU 314, /A LEU 332 Chain-final residues that are actual C termini: /A THR 374 Chain-final residues that are not actual C termini: /A GLU 57, /A GLN 90, /A ALA 159, /A SER 208, /A ARG 251, /A PHE 301, /A LYS 325 193 hydrogen bonds Traceback (most recent call last): File ""/home/purdy/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""/home/purdy/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1313, in __init__ sim_params, residue_templates) File ""/home/purdy/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1409, in _create_openmm_system sys = forcefield.createSystem(top, **system_params) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/simtk/openmm/app/forcefield.py"", line 1114, in createSystem raise Exception('User-supplied template %s does not match the residue %d (%s)' % (tname, res.index+1, res.name)) Exception: User-supplied template CYS does not match the residue 35 (CYS) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/home/purdy/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2676, in _start_sim_or_toggle_pause self.start_sim() File ""/home/purdy/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2696, in start_sim self.params, self.sim_params, excluded_residues = self.ignored_residues) File ""/home/purdy/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 606, in __init__ if self._parse_explicit_template_error(e): File ""/home/purdy/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 644, in _parse_explicit_template_error self.isolde._handle_bad_template(residue) File ""/home/purdy/.local/share/ChimeraX/0.91/site- packages/chimerax/isolde/isolde.py"", line 2784, in _handle_bad_template cmd.cmd_addh(self.session, AtomicStructures([self.selected_model]), hbond=True) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 62, in cmd_addh add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 170, in hbond_add_hydrogens idatm_type, his_Ns, coordinations, in_isolation) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/hbond.py"", line 747, in add_hydrogens _attach_hydrogens(a, altloc_hpos_info, bonding_info) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/hbond.py"", line 892, in _attach_hydrogens add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens, naming_schema) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 875, in add_altloc_hyds pos, bonding_info, alt_loc) File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 901, in new_hydrogen new_h = add_atom(_h_name(parent_atom, h_num, total_hydrogens, naming_schema), ""H"", File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 1023, in _h_name while find_atom(""%s%s"" % (h_name, to_h36(h_num, h_digits))): File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 963, in to_h36 decimal_limit = eval('9' * max_digits) File """", line 0 ^ SyntaxError: unexpected EOF while parsing File """", line 0 ^ SyntaxError: unexpected EOF while parsing File ""/srv/local/progs/chimerax-0.91/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 963, in to_h36 decimal_limit = eval('9' * max_digits) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 418.67 OpenGL renderer: GeForce GTX 1080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Structure Editing nonchimerax all ChimeraX