Morph segmentSieve: empty rList

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6n2y

6n2y title:  
Bacillus PS3 ATP synthase class 1 [more info...]  
  
Chain information for 6n2y #1  
---  
Chain | Description  
A B C | ATP synthase subunit α  
D E F | ATP synthase subunit β  
G | ATP synthase γ chain  
H | ATP synthase ε chain  
I | ATP synthase subunit δ  
a | ATP synthase subunit a  
b1 | ATP synthase subunit b  
b2 | ATP synthase subunit b  
c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c  
  
Non-standard residues in 6n2y #1  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
  

> sequence chain #1/A

Alignment identifier is 1/A  

> log metadata #1

Metadata for 6n2y #1  
---  
Title | Bacillus PS3 ATP synthase class 1  
Citation | Guo, H., Suzuki, T., Rubinstein, J.L. (2019). Structure of a
bacterial ATP synthase. Elife, 8. PMID: 30724163. DOI: 10.7554/eLife.43128  
Non-standard residues | ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
Gene source | Bacillus sp. (strain PS3)  
Experimental method | Electron microscopy  
Resolution | 3.0Å  
  
> hide atoms

> show cartoons

> select :ADP

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

> show sel atoms

> style sel sphere

Changed 27 atom styles  

> select /H

928 atoms, 938 bonds, 129 residues, 1 model selected  

> color sel red

> preset cylinders

Changed 34914 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> save C:\Users\emhab/Desktop/image1.png

Directory "C:\Users\emhab/Desktop" does not exist  

> open 6n2z

Summary of feedback from opening 6n2z fetched from pdb  
---  
note | Fetching compressed mmCIF 6n2z from
http://files.rcsb.org/download/6n2z.cif  
  
6n2z title:  
Bacillus PS3 ATP synthase class 2 [more info...]  
  
Chain information for 6n2z #2  
---  
Chain | Description  
A B C | ATP synthase subunit α  
D E F | ATP synthase subunit β  
G | ATP synthase γ chain  
H | ATP synthase ε chain  
I | Bacillus PS3 ATP synthase subunit δ  
a | Bacillus PS3 ATP synthase subunit a  
b1 | Bacillus PS3 ATP synthase subunit b  
b2 | Bacillus PS3 ATP synthase subunit b  
c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c  
  
Non-standard residues in 6n2z #2  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
  

> open 6n3O

Summary of feedback from opening 6n3O fetched from pdb  
---  
notes | Fetching compressed mmCIF 6n3o from
http://files.rcsb.org/download/6n3o.cif  
Fetching CCD KA7 from http://ligand-expo.rcsb.org/reports/K/KA7/KA7.cif  
  
6n3o title:  
Identification of novel, potent and selective GCN2 inhibitors as first-in-
class anti-tumor agents [more info...]  
  
Chain information for 6n3o #3  
---  
Chain | Description  
A | eIF-2-alpha kinase GCN2  
  
Non-standard residues in 6n3o #3  
---  
KA7 —
N-{3-[(2-aminopyrimidin-5-yl)ethynyl]-2,4-difluorophenyl}-5-chloro-2-methoxypyridine-3-sulfonamide  
  

> morph #1,2

Computed 21 frame morph #4  

> coordset #4 1,21

> hide cartoons

> show atoms

> lighting simple

> coordset #4,1,21

> close #4

> morph #1,2,3 wrap true same true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\morph.py", line 73, in morph  
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph  
res_groups = motion.interpolate(mol, res_interp)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\motion.py", line 107, in interpolate  
results = segment.segmentHingeSame(sm, m, cf, mhs, log=log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\segment.py", line 88, in segmentHingeSame  
segments = find_hinges(parts, fraction, min_hinge_spacing, log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\segment.py", line 298, in find_hinges  
segs = segmentHingeResidues(rList0, rList1, fraction, min_hinge_spacing)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\segment.py", line 306, in segmentHingeResidues  
segments = segmentSieve(rList0, rList1, fraction)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\segment.py", line 41, in segmentSieve  
chain = rList0[0].chain_id  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\segment.py", line 41, in segmentSieve  
chain = rList0[0].chain_id  
  
See log for complete Python traceback.  
  

> morph #1,2,3 wrap true same true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\morph.py", line 73, in morph  
traj = compute_morph(structures, session.logger, method=method, rate=rate,
frames=frames,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\motion.py", line 25, in compute_morph  
res_groups = motion.interpolate(mol, res_interp)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\motion.py", line 107, in interpolate  
results = segment.segmentHingeSame(sm, m, cf, mhs, log=log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\segment.py", line 88, in segmentHingeSame  
segments = find_hinges(parts, fraction, min_hinge_spacing, log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\segment.py", line 298, in find_hinges  
segs = segmentHingeResidues(rList0, rList1, fraction, min_hinge_spacing)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\segment.py", line 306, in segmentHingeResidues  
segments = segmentSieve(rList0, rList1, fraction)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\segment.py", line 41, in segmentSieve  
chain = rList0[0].chain_id  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\morph\segment.py", line 41, in segmentSieve  
chain = rList0[0].chain_id  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 25.20.100.6446
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: HP
Model: HP ENVY x360 Convertible 15m-cn0xxx
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 12,711,006,208
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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[Tom Goddard]

Fixed in 1.3 and 1.4.

User was going the an ATP synthase morph tutorial but opened 6n3o instead of 6n30 and the morph command raised an error because option "same true" was used and no residue numbers in chain A of the wrong structure matched residue numbers of the other two structures. Fixed code to catch this case where no residues match and give a clear error message.