Error that Desired structure doesn't exists

[kskim-phd]

Dear Author,

I sincerely appreciate for your great work in Nature journal!

When I typed the command you instruct : ./data_extract_helix_one.sh 4QVF_B
I got the following error.
Could you please check this?
Thank you very much!

[TobiasPol]

Same problem here.

[zjlclimb]

Same problem here too

[yassermb]

Hi,

In file masif/source/data_preparation/00-pdb_download.py

replace

pdbl = PDBList(server='http://ftp.wwpdb.org')

by

pdbl = PDBList()

[ugeshe]

Hi,

In file masif/source/data_preparation/00-pdb_download.py

replace

pdbl = PDBList(server='http://ftp.wwpdb.org')

by

pdbl = PDBList()

This worked for me

[Hylouis233]

Hi,

In file masif/source/data_preparation/00-pdb_download.py

replace

pdbl = PDBList(server='http://ftp.wwpdb.org')

by

pdbl = PDBList()

The same question, it also worked for me. Thank you!

[Eric-Kobayashi]

Update: the url has changed again.
This works as of Feb 2025:
pdbl = PDBList(server="https://files.wwpdb.org")