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#8553 closed defect (duplicate)

AddH problem

Reported by:	stoddards@…	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:        Windows-10-10.0.22621
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Will not add H atoms to molecules in the file on PC computer (Windows 11), It will do this on my Mac OS X computer

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/stoddards/Desktop/Chem325/1EVE-with-Webina-E20.mol2

Chain information for 1EVE.pdb #1.1  
---  
Chain | Description  
A | No description available  
  
Opened 1EVE-with-Webina-E20.mol2 containing 10 structures (5009 atoms, 4774
bonds)  

> close

> open 1eve format mmcif fromDatabase pdb

1eve title:  
Three dimensional structure of the ANTI-alzheimer drug, E2020 (aricept),
complexed with its target acetylcholinesterase [more info...]  
  
Chain information for 1eve #1  
---  
Chain | Description | UniProt  
A | ACETYLCHOLINESTERASE | ACES_TORCA  
  
Non-standard residues in 1eve #1  
---  
E20 — 1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl)methyl]piperidine (E2020)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  

> open C:/Users/stoddards/Desktop/Chem325/1EVE-Docking-webina_out.pdbqt

Summary of feedback from opening C:/Users/stoddards/Desktop/Chem325/1EVE-
Docking-webina_out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -10.9 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK Name =  
  
Ignored bad PDB record found on line 4  
REMARK 8 active torsions:  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: _1 and _25  
  
238 messages similar to the above omitted  
  
Opened 1EVE-Docking-webina_out.pdbqt containing 9 structures (261 atoms, 288
bonds)  

> select #2

261 atoms, 288 bonds, 9 residues, 10 models selected  

> delete atoms sel

> delete bonds sel

> open C:/Users/stoddards/Desktop/Chem325/1EVE-Docking-webina_out.pdbqt

Summary of feedback from opening C:/Users/stoddards/Desktop/Chem325/1EVE-
Docking-webina_out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -10.9 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK Name =  
  
Ignored bad PDB record found on line 4  
REMARK 8 active torsions:  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: _1 and _25  
  
238 messages similar to the above omitted  
  
Opened 1EVE-Docking-webina_out.pdbqt containing 9 structures (261 atoms, 288
bonds)  

> hide atoms

> set bgColor white

> set bgColor #ffffff00

> hide #3.1 models

> show #3.1 models

> select clear

[Repeated 1 time(s)]

> select #2

1 model selected  

> select #2

1 model selected  

> show atoms

> hide atoms

> select clear

> select #3

261 atoms, 288 bonds, 9 residues, 10 models selected  

> show sel atoms

> select clear

[Repeated 3 time(s)]

> select #1

4748 atoms, 4486 bonds, 936 residues, 1 model selected  

> color sel bychain

> color sel bypolymer

> show sel surfaces

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> set bgColor black

> set bgColor transparent

> show sel surfaces

> color sel bychain

> transparency (#!1 & sel) 60

> transparency (#!1 & sel) 40

> select #3

261 atoms, 288 bonds, 9 residues, 10 models selected  

> select #3

261 atoms, 288 bonds, 9 residues, 10 models selected  

> addcharge H

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge -28) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraXx/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\STODDA~1\AppData\Local\Temp\tmp6qq85t3s\ante.in.mol2 -fi mol2 -o
C:\Users\STODDA~1\AppData\Local\Temp\tmp6qq85t3s\ante.out.mol2 -fo mol2 -c bcc
-nc -28 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(C:\Users\STODDA~1\AppData\Local\Temp\tmp6qq85t3s\ante.in.mol2); atoms read
(29), bonds read (32).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running: "C:/Program Files/ChimeraXx/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraXx/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) `Info: Total number of electrons: 204; net charge: -28`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraXx/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) `/usr/bin/antechamber: Fatal Error!`  
(UNL) `Cannot properly run ""C:/Program Files/ChimeraXx/bin/amber20/bin/sqm"
-O -i sqm.in -o sqm.out".`  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\cmd.py", line 31, in cmd_addcharge  
add_charges(session, residues, method=method, status=session.logger.status,  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 334, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  

> hide sel surfaces

> select #1/A:73@CD

1 atom, 1 residue, 1 model selected  

> select clear

> hide surfaces

> select #3.1

29 atoms, 32 bonds, 1 residue, 1 model selected  

> addcharge H

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge -28) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraXx/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\STODDA~1\AppData\Local\Temp\tmprmbzjvjs\ante.in.mol2 -fi mol2 -o
C:\Users\STODDA~1\AppData\Local\Temp\tmprmbzjvjs\ante.out.mol2 -fo mol2 -c bcc
-nc -28 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(C:\Users\STODDA~1\AppData\Local\Temp\tmprmbzjvjs\ante.in.mol2); atoms read
(29), bonds read (32).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running: "C:/Program Files/ChimeraXx/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraXx/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) `Info: Total number of electrons: 204; net charge: -28`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraXx/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) `/usr/bin/antechamber: Fatal Error!`  
(UNL) `Cannot properly run ""C:/Program Files/ChimeraXx/bin/amber20/bin/sqm"
-O -i sqm.in -o sqm.out".`  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\cmd.py", line 31, in cmd_addcharge  
add_charges(session, residues, method=method, status=session.logger.status,  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 334, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  

> select #3.2

29 atoms, 32 bonds, 1 residue, 1 model selected  

> addcharge H

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge -28) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraXx/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\STODDA~1\AppData\Local\Temp\tmpesmi1i6m\ante.in.mol2 -fi mol2 -o
C:\Users\STODDA~1\AppData\Local\Temp\tmpesmi1i6m\ante.out.mol2 -fo mol2 -c bcc
-nc -28 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(C:\Users\STODDA~1\AppData\Local\Temp\tmpesmi1i6m\ante.in.mol2); atoms read
(29), bonds read (32).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running: "C:/Program Files/ChimeraXx/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraXx/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) `Info: Total number of electrons: 204; net charge: -28`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraXx/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) `/usr/bin/antechamber: Fatal Error!`  
(UNL) `Cannot properly run ""C:/Program Files/ChimeraXx/bin/amber20/bin/sqm"
-O -i sqm.in -o sqm.out".`  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\cmd.py", line 31, in cmd_addcharge  
add_charges(session, residues, method=method, status=session.logger.status,  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 334, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  

> close

> open C:\Users\stoddards\Downloads\Keppra21MBO-webina_out.pdbqt format pdbqt

Summary of feedback from opening C:\Users\stoddards\Downloads\Keppra21MBO-
webina_out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -4.8 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK Name =  
  
Ignored bad PDB record found on line 4  
REMARK 4 active torsions:  
  
Ignored bad PDB record found on line 5  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 6  
REMARK 1 A between atoms: _1 and _2  
  
148 messages similar to the above omitted  
  
Opened Keppra21MBO-webina_out.pdbqt containing 9 structures (126 atoms, 126
bonds)  

> addcharge H

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge -12) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraXx/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\STODDA~1\AppData\Local\Temp\tmpo5pq34f9\ante.in.mol2 -fi mol2 -o
C:\Users\STODDA~1\AppData\Local\Temp\tmpo5pq34f9\ante.out.mol2 -fo mol2 -c bcc
-nc -12 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(C:\Users\STODDA~1\AppData\Local\Temp\tmpo5pq34f9\ante.in.mol2); atoms read
(14), bonds read (14).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running: "C:/Program Files/ChimeraXx/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraXx/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) `Info: Total number of electrons: 92; net charge: -12`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraXx/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) `/usr/bin/antechamber: Fatal Error!`  
(UNL) `Cannot properly run ""C:/Program Files/ChimeraXx/bin/amber20/bin/sqm"
-O -i sqm.in -o sqm.out".`  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\cmd.py", line 31, in cmd_addcharge  
add_charges(session, residues, method=method, status=session.logger.status,  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 334, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
File "C:\Program Files\ChimeraXx\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 598, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.101.2079
OpenGL renderer: Intel(R) UHD Graphics 770
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 5000
OS: Microsoft Windows 11 Enterprise (Build 22621)
Memory: 16,853,479,424
MaxProcessMemory: 137,438,953,344
CPU: 12 12th Gen Intel(R) Core(TM) i5-12500
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0
File attachment: Keppra21MBO-webina_out.pdbqt

Keppra21MBO-webina_out.pdbqt

Attachments (1)

Keppra21MBO-webina_out.pdbqt (15.4 KB ) - added by stoddards@… 3 years ago.: Added by email2trac

Download all attachments as: .zip

Change History (3)

by stoddards@…, 3 years ago

Attachment:	Keppra21MBO-webina_out.pdbqt added

Added by email2trac

comment:1 by Eric Pettersen, 3 years ago

Component:	Unassigned → Structure Editing
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → AddH problem

comment:2 by Eric Pettersen, 3 years ago

Resolution:	→ duplicate
Status:	accepted → closed

Hi Shana,

This is the same issue, you either need to delete the existing hydrogens or do addh first.

--Eric

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