Opened 6 years ago

Closed 6 years ago

#2717 closed defect (nonchimerax)

AddH: can't form new hydrogen name

Reported by: mpurdy@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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 "<string>", 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 "<string>", 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

Change History (3)

in reply to:  1 ; comment:1 by mdp3w@…, 6 years ago 

This was due to a problem with my PDB file. Sorry for the bogus bug report. Thanks for ChimeraX.

Michael

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, January 3, 2020 10:15 AM
To: mpurdy@virginia.edu <mpurdy@virginia.edu>
Subject: [ChimeraX] #2717: ChimeraX bug report submission

#2717: ChimeraX bug report submission
------------------------+-----------------------------
 Reporter:  mpurdy@…    |                Type:  defect
   Status:  new         |            Priority:  normal
Component:  Unassigned  |          Blocked By:
 Blocking:              |  Notify when closed:
------------------------+-----------------------------
 {{{
 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 "<string>", 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 "<string>", 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

 }}}

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2717>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:2 by Eric Pettersen, 6 years ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → AddH: can't form new hydrogen name

comment:3 by Eric Pettersen, 6 years ago

Resolution: → nonchimerax
Status: accepted → closed

Hi Michael,
Glad you were able to resolve the issue yourself. This error happens when an added hydrogen's name would exceed 4 characters if you added a digit to the "base part" of the name. I've seen it happen for other structures that were also in error.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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