MemoryError opening mmCIF

[m.daghan.okur@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

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  

> open C:/Users/user/Downloads/3aok_final.cif

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 563, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1918, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> open C:/Users/user/Downloads/3aok_final.cif

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> open C:/Users/user/Downloads/3aok_final.mtz

Install the Clipper bundle to open "MTZ" format files.  
Opener for format 'MTZ' is not installed; see log for more info  

> open C:/Users/user/Downloads/3aok_final.mtz

Install the Clipper bundle to open "MTZ" format files.  
Opener for format 'MTZ' is not installed; see log for more info  

> open C:/Users/user/Downloads/3aok_final.cif

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> open C:/Users/user/Downloads/3aok_final.cif

Summary of feedback from opening C:/Users/user/Downloads/3aok_final.cif  
---  
warnings | Expected gap or linking atom in THR /A:2 for ALA /A:1  
Expected gap or linking atoms for THR /A:2 and PHE /A:3  
Expected gap or linking atom in PHE /A:3 for GLU /A:4  
Expected gap or linking atom in ILE /A:5 for GLU /A:4  
Expected gap or linking atoms for ILE /A:5 and VAL /A:6  
153 messages similar to the above omitted  
notes | Fetching CCD THR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/THR/THR.cif  
Fetching CCD PHE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/PHE/PHE.cif  
Fetching CCD ILE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/ILE/ILE.cif  
Fetching CCD VAL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/VAL/VAL.cif  
Fetching CCD SER from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/SER/SER.cif  
Fetching CCD TYR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/TYR/TYR.cif  
Fetching CCD TRP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/TRP/TRP.cif  
Fetching CCD LYS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/LYS/LYS.cif  
Fetching CCD LEU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/LEU/LEU.cif  
Fetching CCD PRO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/PRO/PRO.cif  
Fetching CCD MET from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/MET/MET.cif  
Fetching CCD TLA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/TLA/TLA.cif  
Fetching CCD GOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif  
  
3aok_final.cif title:  
Crystal structure of sweet-tasting protein thaumatin II [more info...]  
  
Chain information for 3aok_final.cif #1  
---  
Chain | Description | UniProt  
A | THAUMATIN-2 | THM2_THADA 1-207  
  
Non-standard residues in 3aok_final.cif #1  
---  
GOL — glycerol  
TLA — L(+)-tartaric acid  
  

> open C:/Users/user/Downloads/3wou.pdb

3wou.pdb title:  
Crystal structure of the recombinant thaumatin II At 0.99 A [more info...]  
  
Chain information for 3wou.pdb #2  
---  
Chain | Description | UniProt  
A | thaumatin II | THM2_THADA 1-207  
  
Non-standard residues in 3wou.pdb #2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
TLA — L(+)-tartaric acid  
  

> ui windowfill toggle

[Repeated 2 time(s)]

> lighting full

> ui tool show "Selection Inspector"

> ui mousemode right select

> select #1/A:87

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:88

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/A:132

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:163

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color sel byelement

> show sel atoms

> select #2/A:103

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #2/A:103

10 atoms, 9 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:101

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:125

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:126

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> show sel cartoons

[Repeated 2 time(s)]

> color sel cornflower blue

> color sel red

> color sel forest green

> color sel lime

> select #1/A:125

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:124

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> hide sel atoms

> color sel byelement

> color sel red

> select #2/A:114

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #2/A:113

12 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:125

11 atoms, 10 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2/A:113

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #2/A:112

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #2/A:113

12 atoms, 11 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

[Repeated 1 time(s)]

> select #2/A:113

12 atoms, 11 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel TYR rotLib Dunbrack

3wou.pdb #2/A ASP 113: phi -114.6, psi 136.7 trans  
Changed 180 bond radii  

> swapaa #!2/A:113 TYR criteria 1 rotLib Dunbrack

Using Dunbrack library  
3wou.pdb #!2/A ASP 113: phi -114.6, psi 136.7 trans  
Applying TYR rotamer (chi angles: -66.4 89.0) to 3wou.pdb #!2/A TYR 113  

> swapaa interactive sel TRP rotLib Dunbrack

3wou.pdb #2/A TYR 113: phi -114.6, psi 136.7 trans  
Changed 468 bond radii  

> swapaa #!2/A:113 TRP criteria 1 rotLib Dunbrack

Using Dunbrack library  
3wou.pdb #!2/A TYR 113: phi -114.6, psi 136.7 trans  
Applying TRP rotamer (chi angles: -67.6 89.6) to 3wou.pdb #!2/A TRP 113  

> swapaa interactive sel TRP rotLib Dunbrack

3wou.pdb #2/A TRP 113: phi -114.6, psi 136.7 trans  
Changed 468 bond radii  

> swapaa #!2/A:113 TRP criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
3wou.pdb #!2/A TRP 113: phi -114.6, psi 136.7 trans  
Applying TRP rotamer (chi angles: -67.6 89.6) to 3wou.pdb #!2/A TRP 113  

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:125

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:125

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:113

16 atoms, 17 bonds, 1 residue, 1 model selected  

> select #2/A:113

16 atoms, 17 bonds, 1 residue, 1 model selected  

> select #2/A:113

16 atoms, 17 bonds, 1 residue, 1 model selected  

> select #2/A:113@CA

1 atom, 1 residue, 1 model selected  

> select #1/A:113

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

[Repeated 5 time(s)]

> select #2/A:113@CB

1 atom, 1 residue, 1 model selected  

> hide sel atoms

[Repeated 1 time(s)]

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> hide sel atoms

[Repeated 1 time(s)]

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #1/A:126

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> show sel cartoons

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/A:126@CA

1 atom, 1 residue, 1 model selected  

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #2/A:126

10 atoms, 9 bonds, 1 residue, 1 model selected  

> hide sel atoms

[Repeated 1 time(s)]

> select #2/A:125

24 atoms, 23 bonds, 1 residue, 1 model selected  

> hide sel atoms

[Repeated 1 time(s)]

> select #1/A:176

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:176

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/A:176

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:176

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:176

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel GLU rotLib Dunbrack

3aok_final.cif #1/A LEU 176: phi -72.0, psi -35.6 trans  
Changed 324 bond radii  

> swapaa #!1/A:176 GLU criteria 1 rotLib Dunbrack

Using Dunbrack library  
3aok_final.cif #!1/A LEU 176: phi -72.0, psi -35.6 trans  
Applying GLU rotamer (chi angles: -68.9 177.5 -9.2) to 3aok_final.cif #!1/A
GLU 176  

> swapaa interactive sel GLU rotLib Dunbrack

3aok_final.cif #1/A GLU 176: phi -72.0, psi -35.6 trans  
Changed 324 bond radii  

> swapaa #!1/A:176 GLU criteria 1 rotLib Dunbrack retain false

Using Dunbrack library  
3aok_final.cif #!1/A GLU 176: phi -72.0, psi -35.6 trans  
Applying GLU rotamer (chi angles: -68.9 177.5 -9.2) to 3aok_final.cif #!1/A
GLU 176  

> select #1/A:176

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:173@CG

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select #1/A:176

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel atoms

[Repeated 1 time(s)]

> show sel atoms

> select #1/A:180

5 atoms, 4 bonds, 1 residue, 1 model selected  
Drag select of 3 residues  

> select #1/A:63

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:64

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #2/A:204

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #1/A:132

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/A:201

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select clear

> style sphere

Changed 5379 atom styles  

> style sphere

Changed 5379 atom styles  

> style stick

Changed 5379 atom styles  

> style ball

Changed 5379 atom styles  

> style ball

Changed 5379 atom styles  

> style sphere

Changed 5379 atom styles  

> style stick

Changed 5379 atom styles  

> style sphere

Changed 5379 atom styles  

> style ball

Changed 5379 atom styles  

> style sphere

Changed 5379 atom styles  

> select #2/A:169@CE1

1 atom, 1 residue, 1 model selected  

> select #1/A:163@CE

1 atom, 1 residue, 1 model selected  

> select #2/A:154@CG2

1 atom, 1 residue, 1 model selected  

> style sel stick

Changed 1 atom style  

> style sel stick

Changed 1 atom style  

> style sel stick

Changed 1 atom style  

> select #2/A:113@CH2

1 atom, 1 residue, 1 model selected  

> style sel stick

Changed 1 atom style  

> style sel stick

Changed 1 atom style  

> style sel stick

Changed 1 atom style  

> style sel stick

Changed 1 atom style  

> style sel stick

Changed 1 atom style  

> select clear

> style stick

Changed 5379 atom styles  

> style sphere

Changed 5379 atom styles  

> style stick

Changed 5379 atom styles  

> select #2/A:113

16 atoms, 17 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 16 atom styles  

> style sel sphere

Changed 16 atom styles  

> style sel ball

Changed 16 atom styles  

> style sel stick

Changed 16 atom styles  

> select clear

[Repeated 1 time(s)]

> style sphere

Changed 5379 atom styles  

> select #2/A:113@CH2

1 atom, 1 residue, 1 model selected  

> select clear

> style stick

Changed 5379 atom styles  

> select #2/A:113@NE1

1 atom, 1 residue, 1 model selected  

> select #1/A:115

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select clear

> lighting simple

[Repeated 1 time(s)]

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting simple

> lighting flat

> lighting shadows true intensity 0.5

> lighting flat

[Repeated 4 time(s)]

> select clear

> lighting flat

> lighting full

> lighting flat

[Repeated 2 time(s)]

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

[Repeated 5 time(s)]

> select clear

[Repeated 1 time(s)]

> lighting simple

[Repeated 1 time(s)]

> lighting soft

> lighting simple

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting flat

[Repeated 1 time(s)]

> lighting simple

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> lighting simple

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides fill

> style nucleic stick

Changed 0 atom styles  

> nucleotides slab

> style nucleic stick

Changed 0 atom styles  

> nucleotides tube/slab shape box

> color bynucleotide

> select clear

> hbonds reveal true

5411 hydrogen bonds found  

> hbonds reveal true

5411 hydrogen bonds found  

> hbonds reveal true

5411 hydrogen bonds found  
Drag select of 2 residues, 4 atoms, 19 pseudobonds  
Drag select of 29 atoms, 10 residues, 14 bonds, 76 pseudobonds  
Drag select of 21 atoms, 4 residues, 8 bonds, 57 pseudobonds  

> select clear

> ui tool show Rotamers

> hbonds reveal true

5411 hydrogen bonds found  

> hbonds reveal true

5411 hydrogen bonds found  

> ~hbonds

Drag select of 5 residues  

> rainbow sel

[Repeated 1 time(s)]

> select clear

> rainbow

[Repeated 3 time(s)]

> color bypolymer

> color bychain

> color byhetero

[Repeated 1 time(s)]

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 1 time(s)]Coulombic values for 3aok_final.cif_A SES surface #1.1:
minimum, -12.68, mean 0.21, maximum 13.47  
Coulombic values for 3wou.pdb_A SES surface #2.1: minimum, -12.00, mean 1.99,
maximum 15.92  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color bychain

[Repeated 1 time(s)]

> color bypolymer

> color bychain

> color byhetero

[Repeated 1 time(s)]

> select clear

[Repeated 2 time(s)]

> select #2/A:152@O

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

Invalid texture upload for 0x18bc8f41360 layer=0 mip=0  

> select #2/A

3475 atoms, 3076 bonds, 652 residues, 1 model selected  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Unable to allocate 1.53 MiB for an array with shape (200184,) and data type
int64  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 177, in draw  
self._draw_scene(camera, drawings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 215, in _draw_scene  
shadow, multishadow = self._compute_shadowmaps(opaque_drawings,
transparent_drawings, camera)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 609, in _compute_shadowmaps  
shadow_enabled = r.shadow.use_shadow_map(camera, shadow_drawings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1438, in use_shadow_map  
draw_depth(r, sdrawings, opaque_only = not
r.material.transparent_cast_shadows)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1567, in draw_depth  
draw_opaque(r, drawings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1542, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1555, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 768, in draw  
self.draw_self(renderer, draw_pass)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 775, in draw_self  
self._draw_geometry(renderer, opaque_only = any_transp)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 799, in _draw_geometry  
self._update_buffers()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 925, in _update_buffers  
dss.update_element_buffer(ta, style, tmsel, em)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1774, in update_element_buffer  
e = self.masked_elements(triangles, style, triangle_mask, edge_mask)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1802, in masked_elements  
ta = ta[tmask, :]  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 1.53 MiB for an
array with shape (200184,) and data type int64  
  

Invalid texture upload for 0x18bc8f41360 layer=0 mip=0  

[Repeated 1 time(s)]




OpenGL version: 3.3.0 Core Profile Context 22.20.44.24.221223
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: tr_TR.cp1254
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 82HU
OS: Microsoft Windows 11 Home Single Language (Build 22621)
Memory: 3,588,489,216
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD Ryzen 3 5300U with Radeon Graphics         
OSLanguage: tr-TR

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-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-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
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    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
    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
    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
    pywin32: 305
    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
    WMI: 1.5.1
    zipp: 3.15.0

[Eric Pettersen]

Reported by Muhammed Dağhan Okur

[Greg Couch]

We believe this is fixed in the currently daily build. Please install it and confirm. Thanks.

[Greg Couch]

Duplicated of #8815.