AlphaFold fetch in getting attribute structure.chains

[tic20@…]

Reported by Tristan in comment 5 of ticket #4981:

"open 6w1s; open #1 from alphafold" causes a
traceback in my current installation:

Traceback (most recent call last):

File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-

packages/chimerax/cmd_line/tool.py", line 280, in execute

cmd.run(cmd_text)

File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-

packages/chimerax/core/commands/cli.py", line 2856, in run

result = ci.function(session, kw_args)

File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-

packages/chimerax/open_command/cmd.py", line 118, in cmd_open

models = Command(session, registry=registry).run(provider_cmd_text,

log=log)[0]

File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-

packages/chimerax/core/commands/cli.py", line 2856, in run

result = ci.function(session, kw_args)

File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-

packages/chimerax/open_command/cmd.py", line 150, in provider_open

models, status = collated_open(session, database_name, ident,

File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-

packages/chimerax/open_command/cmd.py", line 433, in collated_open

return remember_data_format()

File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-

packages/chimerax/open_command/cmd.py", line 404, in remember_data_format

models, status = func(*func_args, func_kw)

File "/home/tic20/.local/share/ChimeraX/1.3/site-

packages/chimerax/alphafold/init.py", line 26, in fetch

return fetcher(session, ident, ignore_cache=ignore_cache, kw)

File "/home/tic20/.local/share/ChimeraX/1.3/site-

packages/chimerax/alphafold/fetch_alphafold.py", line 27, in
fetch_alphafold

return fetch_alphafold_for_chains(session, chains,

File "/home/tic20/.local/share/ChimeraX/1.3/site-

packages/chimerax/alphafold/fetch_alphafold.py", line 86, in
fetch_alphafold_for_chains

_rename_chains(alphafold_model, chain)

File "/home/tic20/.local/share/ChimeraX/1.3/site-

packages/chimerax/alphafold/fetch_alphafold.py", line 161, in
_rename_chains

schains = structure.chains

File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-

packages/chimerax/core/attributes.py", line 61, in _getattr_

return base.getattr(self, attr_name, look_in_class=base)

File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-

packages/chimerax/core/attributes.py", line 57, in _getattr_

return look_in_class._attr_registration.get_attr(attr_name)

File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-

packages/chimerax/core/attributes.py", line 83, in get_attr

raise AttributeError("Execution of '%s' object's '%s' property raised

AttributeError" % (self.class_.name, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'chains' property raised
AttributeError

AttributeError: Execution of 'Structure' object's 'chains' property raised
AttributeError

File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 83, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.name, attr_name)) from None

[Tom Goddard]

I do not get this error. Trying

open 6w1s
open #1 from alphafold

works without errors on macOS with July 30 ChimeraX. I am not sure how structure.chains can fail.

Can you reproduce this error? Best to try with current ChimeraX daily build.

[Tom Goddard]

The command to find the alphafold chains is now "alphafold match #1" instead of "open #1 from alphafold".

If this error is not reproducible we will have to wait until we see it again.

[Tristan Croll]

Updated my ChimeraX installation, and fetching the AlphaFold models for 6w1s now works fine.