Opened 4 years ago

Closed 4 years ago

#4859 closed defect (fixed)

AddH: metal may not have alt loc

Reported by: Tristan Croll 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-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.3.dev202106210544 (2021-06-21 05:44:33 UTC)
Description
Failure handling altlocs in addh: 
open 1m2x; addh

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color bychain; color byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3.dev202106210544 (2021-06-21)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1m2x

1m2x title:  
Crystal Structure of the metallo-beta-lactamase BlaB of Chryseobacterium
meningosepticum in complex with the inhibitor D-captopril [more info...]  
  
Chain information for 1m2x #1  
---  
Chain | Description  
A B C D | class B carbapenemase BlaB-1  
  
Non-standard residues in 1m2x #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MCO — 1-(3-mercapto-2-methyl-propionyl)-pyrrolidine-2-carboxylic acid  
NA — sodium ion  
ZN — zinc ion  
  
1m2x mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  

> addh

Summary of feedback from adding hydrogens to 1m2x #1  
---  
notes | Termini for 1m2x (#1) chain A determined from SEQRES records  
Termini for 1m2x (#1) chain B determined from SEQRES records  
Termini for 1m2x (#1) chain C determined from SEQRES records  
Termini for 1m2x (#1) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /A ASP 41, /B ASP 41, /C ASP
41, /D ASP 41  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLN 297, /B GLN 297, /C
GLN 295, /D GLN 297  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2854, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 63, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 214, in add_hydrogens  
_attach_hydrogens(atom, altloc_hpos_info, bonding_info)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 895, in _attach_hydrogens  
add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens,
naming_schema)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 872, in add_altloc_hyds  
h = new_hydrogen(atom, i+1, total_hydrogens, naming_schema,  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 892, in new_hydrogen  
metal_pos = metal.get_alt_loc_coord(alt_loc)  
File "atomic_cpp/cymol.pyx", line 594, in
chimerax.atomic.cymol.CyAtom.get_alt_loc_coord  
ValueError: Atom /A NA 302 NA has no alt loc B  
  
ValueError: Atom /A NA 302 NA has no alt loc B  
  
File "atomic_cpp/cymol.pyx", line 594, in
chimerax.atomic.cymol.CyAtom.get_alt_loc_coord  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 465.19.01
OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        7.3G         44G        327M         10G         54G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
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    ChimeraX-AddH: 2.1.7
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    ChimeraX-Crystal: 1.0
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    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
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    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
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    ChimeraX-MDcrds: 2.3
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    ChimeraX-OpenCommand: 1.6
    ChimeraX-PDB: 2.4.2
    ChimeraX-PDBBio: 1.0
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    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
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    ChimeraX-RotamerLibsDunbrack: 2.0
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    ChimeraX-RotamerLibsRichardson: 2.0
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    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
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    ChimeraX-STL: 1.0
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    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
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    ChimeraX-VolumeMenu: 1.0
    ChimeraX-Voyager: 0.1
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    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
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Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → AddH: metal may not have alt loc

comment:2 by Eric Pettersen, 4 years ago

Resolution: → fixed
Status: accepted → closed

Use main metal position if it doesn't have alt locs. Also, add alt locs if needed to the parent atom so that the hydrogens can be merged into the appropriate "alt loc pool".

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