Delete backbone atom while ribbon displayed: Cylinder end-point and radii arrays must have same size

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.93 (2020-04-03)
Description
(accidentally) deleted a backbone atom while the cartoon was displayed (meant to delete a spurious bond).

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open Atval.pdb

Chain information for Atval.pdb #1  
---  
Chain | Description  
D E H I L M P Q | No description available  
F J N R | No description available  
G K O S | No description available  
  

> open2
> /run/media/tic20/storage/structure_dump/aus/brisbane/guddat/ahas/AtAHAS_val.mrc

Opened AtAHAS_val.mrc, grid size 512,512,512, pixel 0.82, shown at level
0.128, step 2, values float32  

> clipper associate #2 toModel #1

Chain information for Atval.pdb  
---  
Chain | Description  
1.2/D 1.2/E 1.2/H 1.2/I 1.2/L 1.2/M 1.2/P 1.2/Q | No description available  
1.2/F 1.2/J 1.2/N 1.2/R | No description available  
1.2/G 1.2/K 1.2/O 1.2/S | No description available  
  

> addh

Summary of feedback from adding hydrogens to Atval.pdb #1.2  
---  
warnings | Not adding hydrogens to /H LYS 390 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /H GLU 431 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /H LYS 434 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /H LYS 450 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /I LYS 390 CB because it is missing heavy-atom bond
partners  
27 messages similar to the above omitted  
notes | No usable SEQRES records for Atval.pdb (#1.2) chain D; guessing
termini instead  
No usable SEQRES records for Atval.pdb (#1.2) chain E; guessing termini
instead  
No usable SEQRES records for Atval.pdb (#1.2) chain F; guessing termini
instead  
No usable SEQRES records for Atval.pdb (#1.2) chain G; guessing termini
instead  
No usable SEQRES records for Atval.pdb (#1.2) chain H; guessing termini
instead  
11 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /D THR 86, /E THR 86, /F HIS
87, /G LEU 317, /H THR 86, /I THR 86, /J HIS 87, /K LEU 317, /L THR 86, /M THR
86, /N HIS 87, /O LEU 317, /P THR 86, /Q THR 86, /R HIS 87, /S LEU 317  
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: /D ARG 667, /E ARG 667, /F
MET 241, /G SER 475, /H ARG 667, /I ARG 667, /J MET 241, /K SER 475, /L ARG
667, /M ARG 667, /N MET 241, /O SER 475, /P ARG 667, /Q ARG 667, /R MET 241,
/S SER 475  
3580 hydrogen bonds  
/D ARG 667 is not terminus, removing H atom from 'C'  
/E ARG 667 is not terminus, removing H atom from 'C'  
/F MET 241 is not terminus, removing H atom from 'C'  
/G SER 475 is not terminus, removing H atom from 'C'  
/H ARG 667 is not terminus, removing H atom from 'C'  
11 messages similar to the above omitted  
46152 hydrogens added  
  

Unknown command: hhide HC  

> hide HC

> set bgColor white

> dssp

> isolde start

> set selectionWidth 4

Done loading forcefield  

> select #1

92224 atoms, 93152 bonds, 12 models selected  

No template found for residue V106 (VLN)  

Doing nothing  

> show sel

> toolshed show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> save vln_2/VAL.pdb selectedOnly true

Unable to open file 'vln_2/VAL.pdb' for writing  

Invalid "selectedOnly" argument: Expected true or false (or 1 or 0)  

> select #1

92224 atoms, 93152 bonds, 18 models selected  

No template found for residue B729 (FAD)  

Doing nothing  

> show sel

> sequence chain /A

Chains must have same sequence  

> sequence chain /I

Alignment identifier is 1.2.I  

> open 1ybh

Summary of feedback from opening 1ybh fetched from pdb  
---  
notes | Fetching compressed mmCIF 1ybh from
http://files.rcsb.org/download/1ybh.cif  
  
  
  
  
| Summary of feedback from opening /home/tic20/Downloads/ChimeraX/PDB/1ybh.cif  
  
---  
  
  
  
  
notes | Fetching CCD CIE from http://ligand-
expo.rcsb.org/reports/C/CIE/CIE.cif  
Fetching CCD P22 from http://ligand-expo.rcsb.org/reports/P/P22/P22.cif  
  
  
  
  
  
1ybh title:  
Crystal structure of Arabidopsis thaliana Acetohydroxyacid synthase In Complex
With A Sulfonylurea Herbicide Chlorimuron Ethyl [more info...]  
  
Chain information for 1ybh #2  
---  
Chain | Description  
A | Acetolactate synthase, chloroplast  
  
Non-standard residues in 1ybh #2  
---  
CIE —
2-[[[[(4-chloro-6-methoxy-2-pyrimidinyl)amino]carbonyl]amino]sulfonyl]benzoic
acid ethyl ester (chlorimuron ethyl)  
FAD — flavin-adenine dinucleotide  
MG — magnesium ion  
NHE — 2-[N-cyclohexylamino]ethane sulfonic acid (N-cyclohexyltaurine; ches)  
P22 — ethyl dihydrogen diphosphate  
  
1ybh mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| software_defined_assembly  
  
  

> matchmaker #2 to #1/I

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Atval.pdb, chain I (#1.2) with 1ybh, chain A (#2), sequence
alignment score = 2631.8  
RMSD between 498 pruned atom pairs is 1.099 angstroms; (across all 582 pairs:
1.630)  
  

> hide #!1 models

> show #!1 models

> hide #!2 models

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Not adding hydrogens to Atval.pdb #1.2/H LYS 390 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to Atval.pdb #1.2/H GLU 431 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to Atval.pdb #1.2/H LYS 434 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to Atval.pdb #1.2/H LYS 450 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to Atval.pdb #1.2/I LYS 390 CB because it is missing
heavy-atom bond partners  
37 messages similar to the above omitted  
notes | No usable SEQRES records for Atval.pdb (#1.2) chain D; guessing
termini instead  
No usable SEQRES records for Atval.pdb (#1.2) chain E; guessing termini
instead  
No usable SEQRES records for Atval.pdb (#1.2) chain F; guessing termini
instead  
No usable SEQRES records for Atval.pdb (#1.2) chain G; guessing termini
instead  
No usable SEQRES records for Atval.pdb (#1.2) chain H; guessing termini
instead  
11 messages similar to the above omitted  
Chain-initial residues that are actual N termini: Atval.pdb #1.2/D THR 86,
Atval.pdb #1.2/E THR 86, Atval.pdb #1.2/F HIS 87, Atval.pdb #1.2/G LEU 317,
Atval.pdb #1.2/H THR 86, Atval.pdb #1.2/I THR 86, Atval.pdb #1.2/J HIS 87,
Atval.pdb #1.2/K LEU 317, Atval.pdb #1.2/L THR 86, Atval.pdb #1.2/M THR 86,
Atval.pdb #1.2/N HIS 87, Atval.pdb #1.2/O LEU 317, Atval.pdb #1.2/P THR 86,
Atval.pdb #1.2/Q THR 86, Atval.pdb #1.2/R HIS 87, Atval.pdb #1.2/S LEU 317  
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: Atval.pdb #1.2/D ARG 667,
Atval.pdb #1.2/E ARG 667, Atval.pdb #1.2/F MET 241, Atval.pdb #1.2/G SER 475,
Atval.pdb #1.2/H ARG 667, Atval.pdb #1.2/I ARG 667, Atval.pdb #1.2/J MET 241,
Atval.pdb #1.2/K SER 475, Atval.pdb #1.2/L ARG 667, Atval.pdb #1.2/M ARG 667,
Atval.pdb #1.2/N MET 241, Atval.pdb #1.2/O SER 475, Atval.pdb #1.2/P ARG 667,
Atval.pdb #1.2/Q ARG 667, Atval.pdb #1.2/R MET 241, Atval.pdb #1.2/S SER 475  
3375 hydrogen bonds  
Atval.pdb #1.2/D ARG 667 is not terminus, removing H atom from 'C'  
Atval.pdb #1.2/E ARG 667 is not terminus, removing H atom from 'C'  
Atval.pdb #1.2/F MET 241 is not terminus, removing H atom from 'C'  
Atval.pdb #1.2/G SER 475 is not terminus, removing H atom from 'C'  
Atval.pdb #1.2/H ARG 667 is not terminus, removing H atom from 'C'  
11 messages similar to the above omitted  
Termini for 1ybh (#2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: 1ybh #2/A THR 86  
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: 1ybh #2/A ARG 667  
1264 hydrogen bonds  
1ybh #2/A ARG 667 is not terminus, removing H atom from 'C'  
5023 hydrogens added  
  

> select #1

92225 atoms, 93151 bonds, 18 models selected  

No template found for residue B729 (FAD)  

Doing nothing  

> delete sel

No template found for residue B729 (FAD)  

Doing nothing  
Loading residue template for TPP from internal database  

No template found for residue B729 (FAD)  

Doing nothing  

No template found for residue B729 (FAD)  

Doing nothing  

> delete sel

No template found for residue I538 (ASP)  

Doing nothing  

> show sel

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Not adding hydrogens to Atval.pdb #1.2/H LYS 390 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to Atval.pdb #1.2/H GLU 431 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to Atval.pdb #1.2/H LYS 434 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to Atval.pdb #1.2/H LYS 450 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to Atval.pdb #1.2/I LYS 390 CB because it is missing
heavy-atom bond partners  
37 messages similar to the above omitted  
notes | No usable SEQRES records for Atval.pdb (#1.2) chain D; guessing
termini instead  
No usable SEQRES records for Atval.pdb (#1.2) chain E; guessing termini
instead  
No usable SEQRES records for Atval.pdb (#1.2) chain F; guessing termini
instead  
No usable SEQRES records for Atval.pdb (#1.2) chain G; guessing termini
instead  
No usable SEQRES records for Atval.pdb (#1.2) chain H; guessing termini
instead  
11 messages similar to the above omitted  
Chain-initial residues that are actual N termini: Atval.pdb #1.2/D THR 86,
Atval.pdb #1.2/E THR 86, Atval.pdb #1.2/F HIS 87, Atval.pdb #1.2/G LEU 317,
Atval.pdb #1.2/H THR 86, Atval.pdb #1.2/I THR 86, Atval.pdb #1.2/J HIS 87,
Atval.pdb #1.2/K LEU 317, Atval.pdb #1.2/L THR 86, Atval.pdb #1.2/M THR 86,
Atval.pdb #1.2/N HIS 87, Atval.pdb #1.2/O LEU 317, Atval.pdb #1.2/P THR 86,
Atval.pdb #1.2/Q THR 86, Atval.pdb #1.2/R HIS 87, Atval.pdb #1.2/S LEU 317  
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: Atval.pdb #1.2/D ARG 667,
Atval.pdb #1.2/E ARG 667, Atval.pdb #1.2/F MET 241, Atval.pdb #1.2/G SER 475,
Atval.pdb #1.2/H ARG 667, Atval.pdb #1.2/I ARG 667, Atval.pdb #1.2/J MET 241,
Atval.pdb #1.2/K SER 475, Atval.pdb #1.2/L ARG 667, Atval.pdb #1.2/M ARG 667,
Atval.pdb #1.2/N MET 241, Atval.pdb #1.2/O SER 475, Atval.pdb #1.2/P ARG 667,
Atval.pdb #1.2/Q ARG 667, Atval.pdb #1.2/R MET 241, Atval.pdb #1.2/S SER 475  
3375 hydrogen bonds  
Atval.pdb #1.2/D ARG 667 is not terminus, removing H atom from 'C'  
Atval.pdb #1.2/E ARG 667 is not terminus, removing H atom from 'C'  
Atval.pdb #1.2/F MET 241 is not terminus, removing H atom from 'C'  
Atval.pdb #1.2/G SER 475 is not terminus, removing H atom from 'C'  
Atval.pdb #1.2/H ARG 667 is not terminus, removing H atom from 'C'  
11 messages similar to the above omitted  
Termini for 1ybh (#2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: 1ybh #2/A THR 86  
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: 1ybh #2/A ARG 667  
922 hydrogen bonds  
1ybh #2/A ARG 667 is not terminus, removing H atom from 'C'  
4 hydrogens added  
  

> select #1

92226 atoms, 93151 bonds, 18 models selected  

No template found for residue B729 (FAD)  

Doing nothing  

> delete sel

> select #1

92224 atoms, 93149 bonds, 18 models selected  

No template found for residue B730 (FAD)  

Doing nothing  

> select clear

> delete sel

> select #1

92223 atoms, 93148 bonds, 18 models selected  

No template found for residue B731 (FAD)  

Doing nothing  

> delete sel

> select #1

92222 atoms, 93145 bonds, 18 models selected  

No template found for residue B732 (FAD)  

Doing nothing  

> delete :FAD@H11

> select #1

92217 atoms, 93140 bonds, 18 models selected  

No template found for residue D539 (GLY)  

Doing nothing  

> delete sel

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1536, in
_update_graphics_if_needed  
s[i]._update_graphics_if_needed()  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 309, in
_update_graphics_if_needed  
self._update_ribbon_tethers()  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 572, in _update_ribbon_tethers  
rd.update_tethers(self)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 582, in update_tethers  
td.update_tethers(structure)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 614, in update_tethers  
self.positions = _tether_placements(xyz1, xyz2, radii, self._tether_shape)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 627, in _tether_placements  
return _bond_cylinder_placements(c0, c1, radius)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1955, in
_bond_cylinder_placements  
cylinder_rotations(axyz0, axyz1, radii, p)  
ValueError: Cylinder end-point and radii arrays must have same size, got sizes
1204 1203 1203  
  
Error processing trigger "graphics update":  
ValueError: Cylinder end-point and radii arrays must have same size, got sizes
1204 1203 1203  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1955, in
_bond_cylinder_placements  
cylinder_rotations(axyz0, axyz1, radii, p)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
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

[Tom Goddard]

Fixed.

Deleting a CA atom for a residue showing a ribbon caused this error. Redrawing tethers was keeping the position of the deleted atom anchor position on the ribbon. Atoms actually know their ribbon tether position so this extra numpy array of anchor positions was redundant, so I eliminated it, fixing the problem.

Thanks for reporting.