Computing sequence conservation: OSError: [Errno 12] Cannot allocate memory

[francisco.murphy@…]

The following bug report has been submitted:
Platform:        Linux-6.5.5-200.fc38.x86_64-x86_64-with-glibc2.37
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
I am following the tutorial "Analysing and Comparing Structures with UCSF ChimeraX", in the superposition and morphing section I cannot superpose the structures ... (I am only clicking the commands in the html page)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:devel

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> open 3w7f

3w7f title:  
Crystal structure of the C(30) carotenoid dehydrosqualene synthase from
staphylococcus aureus complexed with farnesyl thiopyrophosphate [more info...]  
  
Chain information for 3w7f #1  
---  
Chain | Description | UniProt  
A B | Dehydrosqualene synthase | CRTM_STAAU 1-287  
  
Non-standard residues in 3w7f #1  
---  
FPS — S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen
thiodiphosphate (farnesyl thiopyrophosphate)  
MG — magnesium ion  
  
3w7f mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> delete /b

> view ligand

> label ligand

> label height 1.0

> delete solvent

> label @@display

> distance :21@OG :302@O1B

Distance between /A SER 21 OG and FPS 302 O1B: 2.405Å  

> distance :248@OH :302@O1B

Distance between /A TYR 248 OH and FPS 302 O1B: 2.996Å  

> select :FPS

48 atoms, 46 bonds, 2 residues, 1 model selected  

> hbonds sel restrict cross reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 3w7f
    
    13 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A SER 19 OG    /A FPS 302 O2A  no hydrogen  2.886  N/A
    /A SER 21 N     /A FPS 302 O2B  no hydrogen  3.185  N/A
    /A SER 21 OG    /A FPS 302 O1B  no hydrogen  2.405  N/A
    /A SER 21 OG    /A FPS 302 O2B  no hydrogen  3.332  N/A
    /A TYR 41 OH    /A FPS 302 O2A  no hydrogen  2.585  N/A
    /A ARG 45 NH1   /A FPS 301 O2B  no hydrogen  3.428  N/A
    /A ARG 45 NH1   /A FPS 301 O3B  no hydrogen  2.585  N/A
    /A ARG 45 NH2   /A FPS 301 O2B  no hydrogen  3.175  N/A
    /A ARG 45 NH2   /A FPS 302 O1A  no hydrogen  3.052  N/A
    /A ARG 171 NH1  /A FPS 302 O1B  no hydrogen  2.685  N/A
    /A ARG 171 NH1  /A FPS 302 O3B  no hydrogen  3.412  N/A
    /A ARG 171 NH2  /A FPS 302 O3B  no hydrogen  3.129  N/A
    /A TYR 248 OH   /A FPS 302 O1B  no hydrogen  2.996  N/A
    

  
13 hydrogen bonds found  

> ~hbonds

> ~distance

> contacts sel restrict cross reveal true log true select true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    86 contacts
        atom1           atom2       overlap  distance
    /A FPS 301 C10  /A CYS 44 CB     0.472    3.288
    /A FPS 302 O2A  /A SER 19 CB     0.387    2.913
    /A FPS 301 PB   /A ARG 45 NH1    0.248    3.492
    /A FPS 302 O2A  /A SER 19 CA     0.242    3.058
    /A FPS 302 O1B  /A SER 21 CB     0.215    3.085
    /A FPS 302 C14  /A ALA 157 CB    0.208    3.552
    /A FPS 301 C7   /A CYS 44 CB     0.207    3.433
    /A FPS 302 C14  /A ALA 157 CA    0.191    3.569
    /A FPS 301 C6   /A ASP 48 CB     0.166    3.474
    /A FPS 301 C15  /A TYR 41 CD2    0.158    3.482
    /A FPS 301 O2A  /A MG 303 MG     0.156    1.834
    /A FPS 302 PB   /A ARG 171 NH1   0.139    3.601
    /A FPS 301 PA   /A ASN 168 ND2   0.116    3.624
    /A FPS 301 C14  /A LEU 141 CD1   0.106    3.654
    /A FPS 302 O1A  /A MG 304 MG     0.098    1.892
    /A FPS 301 C8   /A CYS 44 CB     0.097    3.393
    /A FPS 301 O2A  /A ASN 168 OD1   0.097    2.743
    /A FPS 301 O2A  /A ASP 172 OD2   0.088    2.752
    /A FPS 302 O1B  /A SER 21 OG     0.075    2.405
    /A FPS 301 O3B  /A ARG 45 NH1    0.075    2.585
    /A FPS 302 PB   /A SER 21 OG     0.073    3.487
    /A FPS 302 O3B  /A MG 304 MG     0.039    1.951
    /A FPS 301 C15  /A TYR 41 CE2    0.036    3.604
    /A FPS 302 C4   /A GLN 165 OE1   -0.007    3.307
    /A FPS 302 PA   /A ARG 45 NH2    -0.011    3.751
    /A FPS 301 C12  /A TYR 41 CD2    -0.015    3.535
    /A FPS 302 PB   /A SER 21 CB     -0.023    4.003
    /A FPS 302 O1B  /A ARG 171 NH1   -0.025    2.685
    /A FPS 302 C2   /A PHE 22 CE2    -0.038    3.558
    /A FPS 301 C12  /A VAL 137 CG1   -0.048    3.688
    /A FPS 301 O2B  /A MG 304 MG     -0.054    2.044
    /A FPS 301 C2   /A ASP 48 CG     -0.073    3.713
    /A FPS 302 C10  /A GLY 161 CA    -0.084    3.844
    /A FPS 301 C11  /A TYR 41 CD2    -0.091    3.611
    /A FPS 302 C5   /A ALA 134 CB    -0.095    3.855
    /A FPS 301 O1A  /A MG 304 MG     -0.097    2.087
    /A FPS 301 O3B  /A MG 305 MG     -0.103    2.093
    /A FPS 302 C5   /A LEU 164 CB    -0.104    3.864
    /A FPS 302 O2A  /A TYR 41 OH     -0.105    2.585
    /A FPS 301 O3B  /A ASP 48 OD2    -0.105    2.945
    /A FPS 301 C13  /A TYR 41 CD2    -0.106    3.476
    /A FPS 302 C15  /A LEU 145 CD1   -0.106    3.866
    /A FPS 301 C11  /A TYR 41 CE2    -0.107    3.627
    /A FPS 302 C12  /A LEU 160 CD2   -0.110    3.750
    /A FPS 301 C9   /A ARG 45 NH2    -0.149    3.669
    /A FPS 302 C11  /A LEU 164 CD1   -0.154    3.794
    /A FPS 301 C5   /A ASP 48 CG     -0.159    3.919
    /A FPS 302 C1   /A PHE 22 CE2    -0.161    3.681
    /A FPS 301 C9   /A TYR 41 CE2    -0.162    3.802
    /A FPS 302 C1   /A TYR 248 OH    -0.174    3.394
    /A FPS 301 C9   /A ARG 45 CA     -0.175    3.935
    /A FPS 302 C4   /A ASN 168 CB    -0.185    3.945
    /A FPS 302 PB   /A ARG 265 NH2   -0.191    3.931
    /A FPS 302 C14  /A PHE 233 CZ    -0.192    3.832
    /A FPS 302 C4   /A ASN 168 ND2   -0.193    3.713
    /A FPS 302 C15  /A LEU 141 CD1   -0.205    3.965
    /A FPS 302 C4   /A GLN 165 CA    -0.212    3.972
    /A FPS 301 C15  /A MET 15 CE     -0.215    3.975
    /A FPS 302 PA   /A SER 19 CB     -0.217    4.197
    /A FPS 302 O1B  /A TYR 248 CE2   -0.227    3.407
    /A FPS 302 C11  /A GLY 161 CA    -0.230    3.870
    /A FPS 302 C10  /A GLY 138 CA    -0.231    3.991
    /A FPS 302 PA   /A SER 19 CA     -0.232    4.212
    /A FPS 302 C12  /A GLY 138 CA    -0.237    3.877
    /A FPS 302 PA   /A SER 19 OG     -0.239    3.799
    /A FPS 301 C15  /A PHE 22 CD2    -0.249    3.889
    /A FPS 301 C5   /A ASP 48 CB     -0.250    4.010
    /A FPS 301 PA   /A ASN 168 OD1   -0.251    3.771
    /A FPS 302 PA   /A TYR 41 OH     -0.259    3.819
    /A FPS 302 C13  /A LEU 160 CD2   -0.264    3.754
    /A FPS 302 C15  /A LEU 160 CD2   -0.279    4.039
    /A FPS 301 C6   /A ASP 48 CG     -0.284    3.924
    /A FPS 301 C10  /A TYR 41 CD2    -0.296    3.936
    /A FPS 301 C9   /A ARG 45 CZ     -0.312    3.802
    /A FPS 302 C10  /A LEU 141 CD1   -0.317    4.077
    /A FPS 302 O2A  /A TYR 41 CE2    -0.327    3.507
    /A FPS 302 C7   /A ALA 134 CB    -0.333    3.973
    /A FPS 302 PB   /A TYR 248 OH    -0.356    3.916
    /A FPS 302 C10  /A GLY 138 N     -0.356    3.876
    /A FPS 301 O2A  /A ASN 168 CG    -0.361    3.391
    /A FPS 302 C7   /A GLY 161 CA    -0.379    4.019
    /A FPS 302 C14  /A PHE 233 CE1   -0.382    4.022
    /A FPS 302 O2A  /A HIS 18 O      -0.390    3.230
    /A FPS 302 C9   /A LEU 164 CD1   -0.390    4.150
    /A FPS 302 O1A  /A ARG 45 NH2    -0.392    3.052
    /A FPS 302 C6   /A ALA 134 CB    -0.396    4.036
    

  
86 contacts  

> ~select ~protein

45 atoms, 25 residues, 1 model selected  

> info residues sel

residue id /A:15 name MET index 20  
residue id /A:18 name HIS index 23  
residue id /A:19 name SER index 24  
residue id /A:21 name SER index 26  
residue id /A:22 name PHE index 27  
residue id /A:41 name TYR index 46  
residue id /A:44 name CYS index 49  
residue id /A:45 name ARG index 50  
residue id /A:48 name ASP index 53  
residue id /A:134 name ALA index 139  
residue id /A:137 name VAL index 142  
residue id /A:138 name GLY index 143  
residue id /A:141 name LEU index 146  
residue id /A:145 name LEU index 150  
residue id /A:157 name ALA index 162  
residue id /A:160 name LEU index 165  
residue id /A:161 name GLY index 166  
residue id /A:164 name LEU index 169  
residue id /A:165 name GLN index 170  
residue id /A:168 name ASN index 173  
residue id /A:171 name ARG index 176  
residue id /A:172 name ASP index 177  
residue id /A:233 name PHE index 238  
residue id /A:248 name TYR index 253  
residue id /A:265 name ARG index 270  

> ~contacts

> select clear

> open 2zco

2zco title:  
Crystal structure of the C(30) carotenoid dehydrosqualene synthase from
Staphylococcus aureus [more info...]  
  
Chain information for 2zco #2  
---  
Chain | Description | UniProt  
A | Dehydrosqualene synthase | A9JQL9_STAAU 1-287  
  

> preset original

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> mmaker #2 to #1 showAlignment true

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 3w7f, chain A (#1) with 2zco, chain A (#2), sequence alignment
score = 1499.3  
Alignment identifier is 1  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/help_viewer/tool.py", line 320, in intercept  
chimerax_intercept(request_info, *args, session=self.session,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 368, in thread_safe  
func(*args, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2918, in run  
result = ci.function(session, *args, optional=optional,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3457, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 730, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 538, in match  
alignment = session.alignments.new_alignment([s1,s2], None,
auto_associate=None,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/seqalign/manager.py", line 242, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 126, in __init__  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 126, in <listcomp>  
self._headers = [hdr_class(self) for hdr_class in
session.alignments.headers()]  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/alignment_headers/conservation.py", line 42, in __init__  
super().__init__(alignment, *args, eval_while_hidden=True, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py", line 59, in __init__  
self.reevaluate()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/alignment_headers/conservation.py", line 173, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py", line 209, in
reevaluate  
evaluation_func(pos1, pos2)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/alignment_headers/conservation.py", line 295, in
_reeval_al2co  
result = subprocess.run(command, capture_output=True, text=True, check=True)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/subprocess.py", line 505, in
run  
with Popen(*popenargs, **kwargs) as process:  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/subprocess.py", line 951, in
__init__  
self._execute_child(args, executable, preexec_fn, close_fds,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/subprocess.py", line 1754, in
_execute_child  
self.pid = _posixsubprocess.fork_exec(  
OSError: [Errno 12] Cannot allocate memory  
  
OSError: [Errno 12] Cannot allocate memory  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/subprocess.py", line 1754, in
_execute_child  
self.pid = _posixsubprocess.fork_exec(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 23.1.8
OpenGL renderer: Mesa Intel(R) Xe Graphics (TGL GT2)
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: LENOVO
Model: 82FE
OS: Fedora Linux 38 Workstation Edition
Architecture: 64bit 
Virtual Machine: detection failed
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
Cache Size: 12288 KB
Memory:
	MemTotal:        7910328 kB
	MemFree:         1097956 kB
	MemAvailable:    3705772 kB

Graphics:
	unknown

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    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-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    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-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    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: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[Tom Goddard]

The error message says it ran out of memory trying to compute the sequence conservation headers. This is strange. I wonder if the Linux operating system is limiting the memory that ChimeraX can use. It would probably work on a different computer. Or you might try the ChimeraX daily build.

[francisco.murphy@…]

If I run `mm #2 to #1` I get no error, but no alignment. If I include the
`showAlignment true` I get the error. Tried with other structures (lysozyme
8ph8 and 8ph7) and same error.

El lun, 16 oct 2023 a la(s) 12:03, ChimeraX (
ChimeraX-bugs-admin@cgl.ucsf.edu) escribió:

>
>
>
>

[Eric Pettersen]

This works on my Mac, so it must be some problem with running the al2co program (for computing sequence conservation values) on Linux. Will have to try again on a Linux box when I'm onsite on Thursday.

[Eric Pettersen]

I can't reproduce this on an Ubuntu 22.04 system. I guess I suggest installing the ChimeraX daily build, which has some memory-leak problems fixed and see if it's any better. Another possibility is to try to install the flatpak version of ChimeraX.