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#15248 assigned defect

SEQCROW: Buried Volume: Could not find atom

Reported by:	dobromirak@…	Owned by:	Tony Schaefer
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.8rc202405171936 (2024-05-17 19:36:10 UTC)
Description
Hello,

I encountered a bug while trying to create a steric map for buried volume. The log file is attached. Basically, I select the ligand as in this video https://www.youtube.com/watch?v=kPr4uNgMIWo and then I select the atom I want to create the steric map for and the error ("LookupError: Could not find atom: []") in the attached log appears. Since I am interested in finding the steric map for a single atom of an entire molecule in an enzyme pocket the steric map for the entire molecule is not what I want, although if I try for the entire molecule I don't get the error. I tried deleting the rest of the atoms in the molecule and finding the steric map from the buried volume again, but the same error appears.

Best Regards,
Dobromir

Log:
Startup Messages  
---  
notes | available bundle cache has not been initialized yet  
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'  
  
UCSF ChimeraX version: 1.8rc202405171936 (2024-05-17)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\Samaray\Desktop\t.pdb format pdb

Summary of feedback from opening C:\Users\Samaray\Desktop\t.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 2 ALA A 10 1 9  
Start residue of secondary structure not found: HELIX 2 2 ASP A 21 LEU A 29 1
9  
End residue of secondary structure not found: HELIX 3 3 MET A 34 GLN A 40 1 7  
Start residue of secondary structure not found: HELIX 4 4 GLU A 56 ILE A 60 1
5  
Start residue of secondary structure not found: HELIX 5 5 GLU A 63 LEU A 67 1
5  
Start residue of secondary structure not found: HELIX 6 6 SER A 97 LEU A 99 1
3  
Start residue of secondary structure not found: HELIX 7 7 SER A 100 LEU A 109
1 10  
Start residue of secondary structure not found: HELIX 8 8 GLY A 115 THR A 120
1 6  
4 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 5 5 1 LEU A 124 ASP A 134
0  
Start residue of secondary structure not found: SHEET 6 6 1 LEU A 137 LEU A
146 0  
Start residue of secondary structure not found: SHEET 7 7 1 LYS A 149 PHE A
157 0  
  
t.pdb title:  
Chorismate lyase with inhibitor vanillate [more info...]  
  
Chain information for t.pdb #1  
---  
Chain | Description | UniProt  
A | chorismate lyase | UBIC_ECOLI 1-164  
  
Non-standard residues in t.pdb #1  
---  
VNL — 4-hydroxy-3-methoxybenzoate (vanillate)  
  
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> set bgColor white

> lighting full

> graphics silhouettes true

> color byelement

> size /a atomRadius 1.3

Changed 138 atom radii  

> size stickRadius 0.13

Changed 127 bond radii  

> hide cartoons

> show cartoons

> hide cartoons

> hide atoms

> show atoms

> style ball

Changed 138 atom styles  

> ui mousemode right "structure eraser"

> ui mousemode right select

Drag select of 138 atoms, 127 bonds  

> select subtract /A:181@O1

137 atoms, 127 bonds, 17 residues, 1 model selected  

> ui tool show "Buried Volume"

> select clear

> select /A:181@O1

1 atom, 1 residue, 1 model selected  
Traceback (most recent call last):  
File "C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\tools\percent_Vbur.py", line 655, in calc_vbur  
info = percent_vbur_cmd(  
^^^^^^^^^^^^^^^^^  
File "C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\commands\percent_Vbur.py", line 386, in percent_vbur  
results = [d.result() for d in data]  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\commands\percent_Vbur.py", line 386, in <listcomp>  
results = [d.result() for d in data]  
^^^^^^^^^^  
File "C:\Program Files\ChimeraX
1.8rc202405171936\bin\Lib\concurrent\futures\\_base.py", line 456, in result  
return self.__get_result()  
^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX
1.8rc202405171936\bin\Lib\concurrent\futures\\_base.py", line 401, in
__get_result  
raise self._exception  
File "C:\Program Files\ChimeraX
1.8rc202405171936\bin\Lib\concurrent\futures\thread.py", line 58, in run  
result = self.fn(*self.args, **self.kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\SEQCROW\commands\percent_Vbur.py", line 184, in _vbur  
steric_info = rescol.steric_map(  
^^^^^^^^^^^^^^^^^^  
File "C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\geometry.py", line 3058, in steric_map  
key_atoms = self.find(key_atoms)  
^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\geometry.py", line 1374, in find  
raise LookupError(  
LookupError: Could not find atom: [] on  
t.pdb  
138  
  
N 24.13000 -6.89000 35.03400  
C 23.97400 -6.67300 33.59200  
C 22.80900 -7.47800 33.00800  
O 22.98600 -8.20700 32.04400  
C 25.24100 -7.06500 32.85200  
C 26.45000 -6.39800 33.43100  
C 27.74400 -6.76700 32.71200  
O 27.96600 -6.32100 31.56100  
O 28.54200 -7.50300 33.33300  
N 21.62000 -7.32500 33.57200  
C 20.44600 -8.07800 33.08100  
C 19.29300 -7.46700 33.85800  
O 19.52200 -6.73000 34.81300  
C 20.53300 -9.54600 33.52800  
C 19.70400 -10.49400 32.66600  
O 18.95000 -10.04600 31.81000  
O 19.82000 -11.72000 32.82700  
N 18.07400 -7.85000 33.47100  
C 16.80400 -7.47800 34.13800  
C 16.84600 -8.32400 35.44800  
O 17.72900 -9.14600 35.58900  
C 15.63200 -7.97500 33.28000  
O 15.55500 -9.41200 33.36500  
N 15.85900 -8.19200 36.35300  
C 15.82300 -8.94900 37.59700  
C 15.16700 -10.32500 37.51000  
O 15.18400 -11.13600 38.44500  
C 15.09100 -8.08800 38.65200  
C 15.84100 -6.85000 39.04800  
S 17.43400 -7.39700 39.80700  
C 18.44700 -6.20800 38.85400  
N 14.63200 -10.64900 36.34900  
C 13.89600 -11.91700 36.23500  
C 14.52000 -13.19400 36.78700  
O 13.99100 -13.81300 37.72700  
C 13.47900 -12.09600 34.79600  
O 12.63300 -10.97600 34.44500  
C 12.70700 -13.48700 34.61800  
N 6.23200 0.91900 28.18900  
C 5.83600 -0.32200 28.85000  
C 6.07000 -0.16100 30.37200  
O 7.19500 0.09400 30.81000  
C 6.62700 -1.51200 28.27600  
C 6.51400 -2.86100 29.07700  
C 7.65700 -3.78200 28.74900  
N 7.66800 -5.01100 29.49300  
C 6.89200 -6.08100 29.31700  
N 5.95000 -6.13000 28.36900  
N 7.12800 -7.16300 30.09300  
N 6.20100 -6.29300 38.85800  
C 6.70700 -7.65200 38.84100  
C 6.47400 -8.28200 40.19600  
O 6.94100 -7.76700 41.18100  
C 8.18100 -7.66600 38.56900  
C 8.79600 -9.05600 38.26000  
C 8.48000 -9.51500 36.85100  
C 10.25900 -8.94000 38.22500  
N 8.66300 -1.40000 36.89300  
C 9.61600 -1.04000 35.86600  
C 8.98100 -0.25000 34.72100  
O 7.84300 -0.49300 34.39600  
C 10.33400 -2.25100 35.31700  
N 8.13100 -11.53800 31.19800  
C 9.09400 -10.56100 31.72900  
C 10.37200 -10.53500 30.91500  
O 10.87700 -11.59100 30.45700  
C 9.31600 -11.03600 33.14700  
C 9.19400 -12.53500 33.05700  
C 8.19400 -12.82300 31.93900  
N 10.88300 -9.32300 30.74800  
C 12.08500 -9.00300 29.98700  
C 13.33800 -9.66000 30.59300  
O 13.43200 -9.80300 31.79700  
C 12.25000 -7.50000 30.03000  
C 13.14900 -6.85800 29.09000  
C 12.78400 -7.26500 27.65400  
C 12.95400 -5.28800 29.24700  
N 23.96300 -7.08000 22.71400  
C 23.51300 -6.23000 23.79600  
C 24.64200 -5.49100 24.55400  
O 25.70000 -6.05300 24.86000  
C 22.67400 -7.10900 24.70000  
C 21.85100 -6.54900 25.84400  
C 21.30600 -5.20100 25.53800  
C 20.72500 -7.51800 26.08000  
N 25.36500 -1.87800 27.32900  
C 24.76800 -0.86400 28.17700  
C 25.71900 0.32000 28.15400  
O 26.87900 0.14000 28.43900  
C 24.60700 -1.44900 29.57400  
C 24.19900 -0.47200 30.60900  
C 23.81200 -1.24900 31.83100  
N 24.91500 -1.59700 32.68800  
C 24.81000 -2.40200 33.74900  
N 23.63900 -2.96600 34.09900  
N 25.89400 -2.68000 34.46800  
N 17.15600 2.39600 39.71300  
C 18.22700 2.57400 38.75700  
C 17.68300 2.85400 37.35200  
O 16.54700 2.45800 37.05200  
C 19.12400 1.35000 38.73000  
C 18.52300 0.09900 38.09500  
C 19.61400 -0.99800 37.92900  
N 19.00400 -2.13000 37.23700  
C 19.61600 -3.23200 36.84700  
N 20.89100 -3.39500 37.07200  
N 18.92400 -4.16100 36.17100  
N 15.64700 1.95600 30.27400  
C 14.96500 1.03700 31.22500  
C 15.12200 1.57200 32.66900  
O 16.26200 1.75500 33.13100  
C 15.54900 -0.40500 31.09400  
C 15.24700 -1.44300 32.20000  
C 13.76000 -1.82300 32.21600  
C 16.06900 -2.68700 32.01900  
N 13.99600 0.99400 36.81700  
C 13.49200 -0.02500 37.79500  
C 13.43600 0.55600 39.19800  
O 14.35200 1.27400 39.58900  
C 14.43000 -1.25200 37.81700  
C 14.26200 -2.11500 36.60500  
C 15.60700 -2.67300 36.12500  
O 16.54900 -1.90300 35.86800  
O 15.70600 -3.88100 36.03600  
O 9.47700 -4.97700 31.55400  
C 22.05900 -5.25500 30.57100  
C 21.75300 -6.14500 29.58200  
C 21.20700 -4.81400 31.40400  
C 20.41500 -6.60900 29.45800  
C 19.92800 -5.19600 31.36400  
O 19.07700 -4.59600 32.16500  
C 19.49100 -6.09600 30.39600  
C 23.30800 -4.74800 30.65700  
C 19.74900 -3.63400 32.97500  
O 24.27600 -5.08000 29.88200  
O 23.35300 -3.85200 31.51100  
O 18.13000 -6.58000 30.20500  
O 9.28600 -2.26200 31.76200  
  
LookupError: Could not find atom: [] on  
t.pdb  
138  
  
N 24.13000 -6.89000 35.03400  
C 23.97400 -6.67300 33.59200  
C 22.80900 -7.47800 33.00800  
O 22.98600 -8.20700 32.04400  
C 25.24100 -7.06500 32.85200  
C 26.45000 -6.39800 33.43100  
C 27.74400 -6.76700 32.71200  
O 27.96600 -6.32100 31.56100  
O 28.54200 -7.50300 33.33300  
N 21.62000 -7.32500 33.57200  
C 20.44600 -8.07800 33.08100  
C 19.29300 -7.46700 33.85800  
O 19.52200 -6.73000 34.81300  
C 20.53300 -9.54600 33.52800  
C 19.70400 -10.49400 32.66600  
O 18.95000 -10.04600 31.81000  
O 19.82000 -11.72000 32.82700  
N 18.07400 -7.85000 33.47100  
C 16.80400 -7.47800 34.13800  
C 16.84600 -8.32400 35.44800  
O 17.72900 -9.14600 35.58900  
C 15.63200 -7.97500 33.28000  
O 15.55500 -9.41200 33.36500  
N 15.85900 -8.19200 36.35300  
C 15.82300 -8.94900 37.59700  
C 15.16700 -10.32500 37.51000  
O 15.18400 -11.13600 38.44500  
C 15.09100 -8.08800 38.65200  
C 15.84100 -6.85000 39.04800  
S 17.43400 -7.39700 39.80700  
C 18.44700 -6.20800 38.85400  
N 14.63200 -10.64900 36.34900  
C 13.89600 -11.91700 36.23500  
C 14.52000 -13.19400 36.78700  
O 13.99100 -13.81300 37.72700  
C 13.47900 -12.09600 34.79600  
O 12.63300 -10.97600 34.44500  
C 12.70700 -13.48700 34.61800  
N 6.23200 0.91900 28.18900  
C 5.83600 -0.32200 28.85000  
C 6.07000 -0.16100 30.37200  
O 7.19500 0.09400 30.81000  
C 6.62700 -1.51200 28.27600  
C 6.51400 -2.86100 29.07700  
C 7.65700 -3.78200 28.74900  
N 7.66800 -5.01100 29.49300  
C 6.89200 -6.08100 29.31700  
N 5.95000 -6.13000 28.36900  
N 7.12800 -7.16300 30.09300  
N 6.20100 -6.29300 38.85800  
C 6.70700 -7.65200 38.84100  
C 6.47400 -8.28200 40.19600  
O 6.94100 -7.76700 41.18100  
C 8.18100 -7.66600 38.56900  
C 8.79600 -9.05600 38.26000  
C 8.48000 -9.51500 36.85100  
C 10.25900 -8.94000 38.22500  
N 8.66300 -1.40000 36.89300  
C 9.61600 -1.04000 35.86600  
C 8.98100 -0.25000 34.72100  
O 7.84300 -0.49300 34.39600  
C 10.33400 -2.25100 35.31700  
N 8.13100 -11.53800 31.19800  
C 9.09400 -10.56100 31.72900  
C 10.37200 -10.53500 30.91500  
O 10.87700 -11.59100 30.45700  
C 9.31600 -11.03600 33.14700  
C 9.19400 -12.53500 33.05700  
C 8.19400 -12.82300 31.93900  
N 10.88300 -9.32300 30.74800  
C 12.08500 -9.00300 29.98700  
C 13.33800 -9.66000 30.59300  
O 13.43200 -9.80300 31.79700  
C 12.25000 -7.50000 30.03000  
C 13.14900 -6.85800 29.09000  
C 12.78400 -7.26500 27.65400  
C 12.95400 -5.28800 29.24700  
N 23.96300 -7.08000 22.71400  
C 23.51300 -6.23000 23.79600  
C 24.64200 -5.49100 24.55400  
O 25.70000 -6.05300 24.86000  
C 22.67400 -7.10900 24.70000  
C 21.85100 -6.54900 25.84400  
C 21.30600 -5.20100 25.53800  
C 20.72500 -7.51800 26.08000  
N 25.36500 -1.87800 27.32900  
C 24.76800 -0.86400 28.17700  
C 25.71900 0.32000 28.15400  
O 26.87900 0.14000 28.43900  
C 24.60700 -1.44900 29.57400  
C 24.19900 -0.47200 30.60900  
C 23.81200 -1.24900 31.83100  
N 24.91500 -1.59700 32.68800  
C 24.81000 -2.40200 33.74900  
N 23.63900 -2.96600 34.09900  
N 25.89400 -2.68000 34.46800  
N 17.15600 2.39600 39.71300  
C 18.22700 2.57400 38.75700  
C 17.68300 2.85400 37.35200  
O 16.54700 2.45800 37.05200  
C 19.12400 1.35000 38.73000  
C 18.52300 0.09900 38.09500  
C 19.61400 -0.99800 37.92900  
N 19.00400 -2.13000 37.23700  
C 19.61600 -3.23200 36.84700  
N 20.89100 -3.39500 37.07200  
N 18.92400 -4.16100 36.17100  
N 15.64700 1.95600 30.27400  
C 14.96500 1.03700 31.22500  
C 15.12200 1.57200 32.66900  
O 16.26200 1.75500 33.13100  
C 15.54900 -0.40500 31.09400  
C 15.24700 -1.44300 32.20000  
C 13.76000 -1.82300 32.21600  
C 16.06900 -2.68700 32.01900  
N 13.99600 0.99400 36.81700  
C 13.49200 -0.02500 37.79500  
C 13.43600 0.55600 39.19800  
O 14.35200 1.27400 39.58900  
C 14.43000 -1.25200 37.81700  
C 14.26200 -2.11500 36.60500  
C 15.60700 -2.67300 36.12500  
O 16.54900 -1.90300 35.86800  
O 15.70600 -3.88100 36.03600  
O 9.47700 -4.97700 31.55400  
C 22.05900 -5.25500 30.57100  
C 21.75300 -6.14500 29.58200  
C 21.20700 -4.81400 31.40400  
C 20.41500 -6.60900 29.45800  
C 19.92800 -5.19600 31.36400  
O 19.07700 -4.59600 32.16500  
C 19.49100 -6.09600 30.39600  
C 23.30800 -4.74800 30.65700  
C 19.74900 -3.63400 32.97500  
O 24.27600 -5.08000 29.88200  
O 23.35300 -3.85200 31.51100  
O 18.13000 -6.58000 30.20500  
O 9.28600 -2.26200 31.76200  
  
File "C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\AaronTools\geometry.py", line 1374, in find  
raise LookupError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 528.49
OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Pro (Build 18362)
Memory: 34,291,212,288
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-9900KF CPU @ 3.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57
    ChimeraX-AtomicLibrary: 14.0.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.4
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.4
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8rc202405171936
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.3
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    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-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.16
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.3
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.51.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.0
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    Send2Trash: 1.8.3
    SEQCROW: 1.8.8
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 17 months ago

Component:	Unassigned → Third Party
Owner:	set to Tony Schaefer
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → SEQCROW: Buried Volume: Could not find atom

Reported by Dobromir Antonov Kalchevski

comment:2 by Tony Schaefer, 17 months ago

Dobromir,

The steric map code seems to assume the center atom has at least one bond.
I'll fix that soon. In the meantime, bond the central atom to anything else
and check the box for 'use display orientation' option in the tool's
settings.

Best,

Tony

On Mon, May 20, 2024 at 12:31 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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