getpdb doesn't work anymore - shutdown on 9th december 2020 - How to replace it?

Hello,

I was using information from protein data bank in my project.

It was quite simple I just have to write:

S = getpdb('1CIV')

Unfortunately yesterday (9th dec) I got message:

The server returned the status 404 with message "Not Found" in response to the request to URL

http://www.rcsb.org/pdb/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1CIV.

When I check the site it shows me

It has been permanently removed as part of our announced shutdown on December 9th, 2020.

Apparently there is new json-based API. I'm not sure how to use it in matlab.

Do you have any ideas where I should start? What I should read to learn how to use it in matlab? There are some links on the site but I don't quite understand them(https://data.rcsb.org/#data-api) (http://www.rcsb.org/pages/webservices)

I would be very grateful for any points because big part of my student project just fell apart

[Rik]

You could also consider using the REST-based API instead. I suspect that will be closer to what getpdb was doing.

This bugreport (which was linked in the sidebar) may also be of help.

[Karolina Cicha]

Thank you very much! Bugreport was very helpful.

[Rik]

You should post your solution as an answer and accept it. That way others can find the solution much more easily.

Answer 1

[Karolina Cicha]

websave('1CIV.pdb', 'https://files.rcsb.org/download/1CIV.pdb');
x = pdbread('1CIV.pdb')