Opened 2 years ago

Closed 2 years ago

Last modified 2 years ago

#9600 closed defect (duplicate)

Color by attribute failure

Reported by: suhu.bh1421@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
On selecting the protein and going to 'Render by Attribute' option, after chosing residues, there is no attribute for kdHydrophobicity in the chose Attributes drop down menu.

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 8K3R

Traceback (most recent call last):  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 97, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open  
return remember_data_format()  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\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 8K3R format mmcif fromDatabase pdb

Traceback (most recent call last):  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\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 "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\gui.py", line 368, in thread_safe  
func(*args, **kw)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 97, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open  
return remember_data_format()  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\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 8K3R format mmcif fromDatabase pdb

Traceback (most recent call last):  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\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 "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\gui.py", line 368, in thread_safe  
func(*args, **kw)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 97, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open  
return remember_data_format()  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\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 8K3R

Traceback (most recent call last):  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 97, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open  
return remember_data_format()  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\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/ASK/OneDrive/Desktop/Comparative analysis of processive
> glycosyl transferases/PDB files/8k3r.cif"

Traceback (most recent call last):  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\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 8K3R

8k3r title:  
S. cerevisiae Chs1 in apo state incubated with GlcNAc [more info...]  
  
Chain information for 8k3r #1  
---  
Chain | Description | UniProt  
A B | Chitin synthase 1 | CHS1_YEAST 1-1131  
  
Non-standard residues in 8k3r #1  
---  
POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl
2-(trimethylammonio)ethyl phosphate (POPC)  
  

> select #ChainA

Expected an objects specifier or a keyword  

> select /A

5530 atoms, 5661 bonds, 5 pseudobonds, 703 residues, 2 models selected  

> color (#!1 & sel) forest green

> select /B

5531 atoms, 5662 bonds, 5 pseudobonds, 703 residues, 2 models selected  

> color (#!1 & sel) purple

> select clear

> select sequence "T969 to T1024"

Nothing selected  

> help help:user

[Repeated 1 time(s)]

> ui tool show "Show Sequence Viewer"

> sequence chain /A /B

Alignment identifier is 1  

> select /A-B:969

28 atoms, 30 bonds, 2 residues, 1 model selected  

> select /A-B:969-1015

548 atoms, 556 bonds, 2 pseudobonds, 80 residues, 2 models selected  

> focus

Unknown command: focus  

> focus protein

Unknown command: focus protein  

> focus protein

Unknown command: focus protein  

> select /A

5530 atoms, 5661 bonds, 5 pseudobonds, 703 residues, 2 models selected  

> delete

Missing or invalid "atoms" argument: empty atom specifier  

> delete ChainA

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> open 8K3R

8k3r title:  
S. cerevisiae Chs1 in apo state incubated with GlcNAc [more info...]  
  
Chain information for 8k3r #2  
---  
Chain | Description | UniProt  
A B | Chitin synthase 1 | CHS1_YEAST 1-1131  
  
Non-standard residues in 8k3r #2  
---  
POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl
2-(trimethylammonio)ethyl phosphate (POPC)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B #2/A #2/B

Alignment identifier is 1  

> select #2/B

5531 atoms, 5662 bonds, 5 pseudobonds, 703 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #1/B

5531 atoms, 5662 bonds, 5 pseudobonds, 703 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> select add #2

5530 atoms, 5661 bonds, 5 pseudobonds, 703 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select /A:375

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

> select /A:375-385

84 atoms, 85 bonds, 11 residues, 1 model selected  

> select /A:674

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

> select /A:674-683

77 atoms, 80 bonds, 10 residues, 1 model selected  

> select
> /A:392-401,410-414,424-428,435-439,458-478,488-491,506-517,577-594,610-621,636-669,683-696,706-726,749-781,784-828,830-856,861-892,909-932,936-963,997-1012,1027-1060,1063-1075,1091-1125

3587 atoms, 3662 bonds, 448 residues, 1 model selected  

> select /A:663-664

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:663-665

23 atoms, 22 bonds, 3 residues, 1 model selected  

> select /A:645

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

> select /A:645-668

194 atoms, 197 bonds, 24 residues, 1 model selected  

> color sel hot pink

> toolshed show

> label sel atoms attribute name

> select /A:750

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

> select /A:750-780

278 atoms, 290 bonds, 31 residues, 1 model selected  

> color sel lime

> select /A:934

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

> select /A:934-963

250 atoms, 258 bonds, 30 residues, 1 model selected  

> color sel yellow

> open 8K3R

8k3r title:  
S. cerevisiae Chs1 in apo state incubated with GlcNAc [more info...]  
  
Chain information for 8k3r #1  
---  
Chain | Description | UniProt  
A B | Chitin synthase 1 | CHS1_YEAST 1-1131  
  
Non-standard residues in 8k3r #1  
---  
POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl
2-(trimethylammonio)ethyl phosphate (POPC)  
  

> select #2/A:989

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

> select #2/A:989-992

29 atoms, 29 bonds, 4 residues, 1 model selected  

> color sel red

> select add #1

11090 atoms, 11352 bonds, 10 pseudobonds, 1410 residues, 3 models selected  

> select #2/A:376

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

> select #2/A:376-380

41 atoms, 41 bonds, 5 residues, 1 model selected  

> color sel forest green

> select add #2

5530 atoms, 5661 bonds, 5 pseudobonds, 703 residues, 3 models selected  

> select subtract #2

Nothing selected  

> hide #!2 models

> show #!2 models

> hide #!1 models

> select
> #2/A:376-377,386-390,415-421,448-454,493-499,527-528,531-532,535-542,545-549,554-557,565-572,597-602,606-607,624-633,679-682,733-744,981-982,991-992

728 atoms, 720 bonds, 95 residues, 1 model selected  

> select #2/A:453

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

> select #2/A:453-457

44 atoms, 44 bonds, 5 residues, 1 model selected  

> color sel orange red

> select
> #2/A:392-401,410-414,424-428,435-439,458-478,488-491,506-517,577-594,610-621,636-669,683-696,706-726,749-781,784-828,830-856,861-892,909-932,936-963,997-1012,1027-1060,1063-1075,1091-1125

3587 atoms, 3662 bonds, 448 residues, 1 model selected  

> select #2/A:578

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

> select #2/A:578

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

> color sel white

> select #2/A:450-455

49 atoms, 49 bonds, 6 residues, 1 model selected  

> select #2/A:450-455

49 atoms, 49 bonds, 6 residues, 1 model selected  

> select #2/A:455

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

> select #2/A:455

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

> select #2/A:751

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

> select #2/A:751-759

85 atoms, 86 bonds, 9 residues, 1 model selected  

> color sel lime

> color sel red

> select #2/A:651

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

> select #2/A:651

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

> color sel purple

> select #2/A:453

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

> select #2/A:453-455

27 atoms, 27 bonds, 3 residues, 1 model selected  

> color sel purple

> select #2/A:578

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

> select #2/A:578

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

> color sel purple

> select #2/A:756

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

> select #2/A:756-759

42 atoms, 41 bonds, 4 residues, 1 model selected  

> color sel purple

> select
> #2/A:392-401,410-414,424-428,435-439,458-478,488-491,506-517,577-594,610-621,636-669,683-696,706-726,749-781,784-828,830-856,861-892,909-932,936-963,997-1012,1027-1060,1063-1075,1091-1125

3587 atoms, 3662 bonds, 448 residues, 1 model selected  

> select #2/A:654

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

> select #2/A:654-655

21 atoms, 21 bonds, 2 residues, 1 model selected  

> color sel purple

> select #2/A:760

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

> select #2/A:760

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

> color sel purple

> select #2/A:718

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

> select #2/A:718

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

> color sel purple

> select #2/A:673

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

> select #2/A:673-677

28 atoms, 28 bonds, 5 residues, 1 model selected  

> color sel purple

> select #2/A:675

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

> select #2/A:675

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

> show (sel-residues & sidechain) target ab

> select
> #2/A:392-401,410-414,424-428,435-439,458-478,488-491,506-517,577-594,610-621,636-669,683-696,706-726,749-781,784-828,830-856,861-892,909-932,936-963,997-1012,1027-1060,1063-1075,1091-1125

3587 atoms, 3662 bonds, 448 residues, 1 model selected  

> select #2/A:760

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

> select #2/A:760

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

> show (sel-residues & sidechain) target ab

> select add #2/A:662

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select subtract #2/A:662

14 atoms, 15 bonds, 1 residue, 1 model selected  
Drag select of 2 atoms, 4 residues, 1 bonds  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> select add #2/A:675@CB

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select up

21 atoms, 22 bonds, 2 residues, 1 model selected  

> ui tool show Contacts

> contacts ignoreHiddenModels true

2971 contacts  

> undo

> select clear

> ui tool show Clashes

> hide target m

[Repeated 1 time(s)]

> show target m

> hide #3 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> select #2/A:457

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

> select #2/A:457

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

> color sel dark gray

> select #2/A:602

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

> select #2/A:602

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

> color sel gray

> select #2/A:600

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

> select #2/A:600-605

40 atoms, 39 bonds, 3 pseudobonds, 6 residues, 2 models selected  

> select #2/A:605

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

> select #2/A:605

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

> color sel gray

> select #2/A:745

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

> select #2/A:745

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

> color sel gray

> select #2/A:457

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

> select add #2/A:618

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select subtract #2/A:618

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

> select add #2/A:745

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add #2/A:602

25 atoms, 22 bonds, 3 residues, 1 model selected  

> select add #2/A:605

32 atoms, 28 bonds, 4 residues, 1 model selected  

> ui tool show Distances

> distance style color #9bffc0

[Repeated 2 time(s)]

> distance style color #9dffbe

[Repeated 2 time(s)]

> distance style color #e0ffbe

[Repeated 2 time(s)]

> distance style color #e2ffc0

[Repeated 2 time(s)]

> distance style color #e2ffc1

[Repeated 2 time(s)]

> distance style color #758464

[Repeated 2 time(s)]

> distance style decimalPlaces 8

[Repeated 2 time(s)]

> distance style radius 8

[Repeated 2 time(s)]Exactly two atoms must be selected!  

> select clear

> select #2/A:457

9 atoms, 8 bonds, 1 residue, 1 model selected  
Drag select of 6 residues  

> select clear

[Repeated 1 time(s)]

> select #2/A:457

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

> select add #2/A:745

17 atoms, 15 bonds, 2 residues, 1 model selected  
Exactly two atoms must be selected!  

> distance style decimalPlaces 1

[Repeated 2 time(s)]

> set bgColor white

> set bgColor #ffffff00

> set bgColor black

> set bgColor transparent

> select down

17 atoms, 15 bonds, 2 residues, 1 model selected  

> ui tool show Contacts

> contacts ignoreHiddenModels true color #778b70

2971 contacts  

> show #3 models

> hide #3 models

> select #2/A:602-603

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #2/A:602-604

17 atoms, 16 bonds, 3 residues, 1 model selected  

> select #2/A:456

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

> select #2/A:456-457

17 atoms, 16 bonds, 1 pseudobond, 2 residues, 2 models selected  

> select clear

> select #2/A:456

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

> select #2/A:456-457

17 atoms, 16 bonds, 1 pseudobond, 2 residues, 2 models selected  

> select #2/A:602

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

> select #2/A:602

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

> select #2/A:456

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

> select #2/A:456-457

17 atoms, 16 bonds, 1 pseudobond, 2 residues, 2 models selected  

> color (#!2 & sel) magenta

> ui tool show "Color Actions"

> color sel dark olive green

> select #2/A:602

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

> select #2/A:602

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

> color sel dark olive green

> undo

> color sel dark olive green

> select #2/A:752

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

> select #2/A:752

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

> color sel dark olive green

> select #2/A:657

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

> select #2/A:657-658

14 atoms, 13 bonds, 2 residues, 1 model selected  

> color sel gold

> select #2/A:662

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

> select #2/A:662

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

> color sel gold

> select #2/A:673

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

> select #2/A:673

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

> color sel gold

> select #2/A:674

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

> select #2/A:674

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

> color sel gold

> select #2/A:675

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

> select #2/A:675

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

> color sel gold

> select #2/A:676

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

> select #2/A:676

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

> color sel gold

> select #2/A:718

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

> select #2/A:718

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

> color sel gold

> select #2/A:760

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

> select #2/A:760

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

> color sel gold

> select #2/A:578

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

> select #2/A:578

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

> color sel spring green

> select #2/A:745

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

> select #2/A:745

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

> color sel spring green

> select #2/A:756

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

> select #2/A:756

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

> color sel spring green

> select #2/A:759

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

> select #2/A:759

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

> color sel spring green

> select #2/A:675

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

> select #2/A:675

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

> color sel slate blue

> select #2/A:675

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

> select #2/A:675

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

> color sel red

> color sel dark slate blue

> select up

9 atoms, 8 bonds, 2 residues, 1 model selected  

> select up

21 atoms, 22 bonds, 2 residues, 1 model selected  

> ui tool show Contacts

> contacts ignoreHiddenModels true color #778b70

2971 contacts  

> show #3 models

> select #2/A:673

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

> select #2/A:673-675

19 atoms, 19 bonds, 3 residues, 1 model selected  

> select #2/A:673

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

> select #2/A:673-676

23 atoms, 23 bonds, 4 residues, 1 model selected  

> color sel light salmon

> select #2/A:673

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

> select #2/A:673-676

23 atoms, 23 bonds, 4 residues, 1 model selected  

> color sel light salmon

> select #2/A:653

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

> select #2/A:653

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

> color sel saddle brown

> select #2/A:657

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

> select #2/A:657

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

> color sel saddle brown

> select #2/A:661

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

> select #2/A:661

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

> color sel saddle brown

> select #2/A:801

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

> select #2/A:801

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

> color sel saddle brown

> select #2/A:805

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

> select #2/A:805

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

> color sel saddle brown

> select #2/A:808

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

> select #2/A:808

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

> color sel saddle brown

> ui tool show "Render By Attribute"

> ui tool show Registration

Registration server unavailable. Please try again later.  
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  

Failed to subscribed suhu.bh1421@gmail.com to the ChimeraX discussion list:
HTTP Error 404: Not Found  

Failed to subscribed suhu.bh1421@gmail.com to the ChimeraX announcements list:
HTTP Error 404: Not Found  

> ui tool show Registration

Your copy of Chimera is already registered through 08/18/24.  
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  

Failed to subscribed suhani.bhattacharyya@students.iiserpune.ac.in to the
ChimeraX discussion list: HTTP Error 404: Not Found  

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> color byattribute r:chi1 #!1 target csab palette
> -179.949,blue:-0.0707734,white:179.808,red

Traceback (most recent call last):  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 217, in render  
self._cur_attr_info().render(self.session, attr_name, models, method, params,  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\atomic\\__init__.py", line 184, in render  
run(session, "color byattr %s:%s %s target %s %s%s" % (prefix, attr_name,
spec, letters,  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1144, in color_by_attr  
acolors = _value_colors(palette, range, attr_vals)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1305, in _value_colors  
min_val, max_val = min(values), max(values)  
TypeError: '<' not supported between instances of 'NoneType' and 'NoneType'  
  
TypeError: '  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1305, in _value_colors  
min_val, max_val = min(values), max(values)  
  
See log for complete Python traceback.  
  

> select #1/A

5530 atoms, 5661 bonds, 5 pseudobonds, 703 residues, 2 models selected  

> select #1/A#1/B#2/A

16591 atoms, 16984 bonds, 2986 pseudobonds, 2109 residues, 5 models selected  

> color byattribute r:chi1 #!1 target csab palette
> -179.949,blue:-0.0707734,white:179.808,red

Traceback (most recent call last):  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 174, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self.render(apply=True))  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 217, in render  
self._cur_attr_info().render(self.session, attr_name, models, method, params,  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\atomic\\__init__.py", line 184, in render  
run(session, "color byattr %s:%s %s target %s %s%s" % (prefix, attr_name,
spec, letters,  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1144, in color_by_attr  
acolors = _value_colors(palette, range, attr_vals)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1305, in _value_colors  
min_val, max_val = min(values), max(values)  
TypeError: '<' not supported between instances of 'NoneType' and 'NoneType'  
  
TypeError: '  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1305, in _value_colors  
min_val, max_val = min(values), max(values)  
  
See log for complete Python traceback.  
  

> color byattribute r:chi2 #!1 target csab palette
> -179.938,blue:0.0134649,white:179.965,red

Traceback (most recent call last):  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 174, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self.render(apply=True))  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 217, in render  
self._cur_attr_info().render(self.session, attr_name, models, method, params,  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\atomic\\__init__.py", line 184, in render  
run(session, "color byattr %s:%s %s target %s %s%s" % (prefix, attr_name,
spec, letters,  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1144, in color_by_attr  
acolors = _value_colors(palette, range, attr_vals)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1305, in _value_colors  
min_val, max_val = min(values), max(values)  
TypeError: '<' not supported between instances of 'NoneType' and 'float'  
  
TypeError: '  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1305, in _value_colors  
min_val, max_val = min(values), max(values)  
  
See log for complete Python traceback.  
  

> color byattribute r:chi2 #!1 target csab palette
> -79.2658,blue:0.0134649,white:65.4504,red

Traceback (most recent call last):  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 174, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self.render(apply=True))  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 217, in render  
self._cur_attr_info().render(self.session, attr_name, models, method, params,  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\atomic\\__init__.py", line 184, in render  
run(session, "color byattr %s:%s %s target %s %s%s" % (prefix, attr_name,
spec, letters,  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1144, in color_by_attr  
acolors = _value_colors(palette, range, attr_vals)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1305, in _value_colors  
min_val, max_val = min(values), max(values)  
TypeError: '<' not supported between instances of 'NoneType' and 'float'  
  
TypeError: '  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1305, in _value_colors  
min_val, max_val = min(values), max(values)  
  
See log for complete Python traceback.  
  

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

16447 atoms, 16843 bonds, 2952 pseudobonds, 2106 residues, 5 models selected  

> select ::name="GLU"

891 atoms, 780 bonds, 10 pseudobonds, 111 residues, 3 models selected  

> color byattribute r:seq_conservation #!1 target csab palette
> -79.2658,blue:0.0134649,white:65.4504,red

All 'seq_conservation' values are None  

> ui tool show "Render By Attribute"

[Repeated 1 time(s)]No attribute chosen for rendering  
Traceback (most recent call last):  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 174, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self.render(apply=True))  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 206, in render  
markers.coord_type = "absolute"  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 941, in coord_type  
self._convert_coords()  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 1100, in _convert_coords  
m.xy = conv_func(m.xy)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 707, in _rel2abs  
abs_x = self._min_val * (1-x) + x * self._max_val  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
AttributeError: 'MarkedHistogram' object has no attribute '_min_val'  
  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 707, in _rel2abs  
abs_x = self._min_val * (1-x) + x * self._max_val  
  
See log for complete Python traceback.  
  

> color byattribute r:omega #!1-2 & sel target csab palette
> 0,blue:0.5,white:1,red

Traceback (most recent call last):  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 174, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self.render(apply=True))  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 217, in render  
self._cur_attr_info().render(self.session, attr_name, models, method, params,  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\atomic\\__init__.py", line 184, in render  
run(session, "color byattr %s:%s %s target %s %s%s" % (prefix, attr_name,
spec, letters,  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1144, in color_by_attr  
acolors = _value_colors(palette, range, attr_vals)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1305, in _value_colors  
min_val, max_val = min(values), max(values)  
TypeError: '<' not supported between instances of 'NoneType' and 'float'  
  
TypeError: '  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1305, in _value_colors  
min_val, max_val = min(values), max(values)  
  
See log for complete Python traceback.  
  

> color byattribute r:omega #!1-2 & sel target csab palette
> -179.996,blue:-0.0146585,white:179.966,red

Traceback (most recent call last):  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 174, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda: self.render(apply=True))  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 217, in render  
self._cur_attr_info().render(self.session, attr_name, models, method, params,  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\atomic\\__init__.py", line 184, in render  
run(session, "color byattr %s:%s %s target %s %s%s" % (prefix, attr_name,
spec, letters,  
File "C:\Users\ASK\Documents\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:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1144, in color_by_attr  
acolors = _value_colors(palette, range, attr_vals)  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1305, in _value_colors  
min_val, max_val = min(values), max(values)  
TypeError: '<' not supported between instances of 'NoneType' and 'float'  
  
TypeError: '  
File "C:\Users\ASK\Documents\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1305, in _value_colors  
min_val, max_val = min(values), max(values)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 81W8
OS: Microsoft Windows 11 Home Single Language (Build 22621)
Memory: 4,080,263,168
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-1005G1 CPU @ 1.20GHz
OSLanguage: en-US

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

Change History (3)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Color by attribute failure

comment:2 by Eric Pettersen, 2 years ago

Resolution: → duplicate
Status: accepted → closed

Hi Suhani,

Thanks for reporting this problem. It has been fixed in the daily build, so if you get that then things will work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Eric Pettersen, 2 years ago

Hi Suhani,

I missed the part where you were asking about kdHydrophobicity in Render by Attribute. kdHydrophobicity is not a builtin attribute for ChimeraX, so you have to define it by opening an attribute-definition file as described here: ​https://www.cgl.ucsf.edu/chimerax/docs/user/formats/defattr.html . Once you've done that, then it will appear in the Render by Attribute tool.

--Eric

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