mkdssp is not generating SS assignment on alpha fold pdb files

[iqbals]

Hi - I have a DSSP set up in my Mac which works perfectly. This is the command I use: mkdssp 1mot.pdb -o 1mot.dssp

But that same command is not generating any SS assignment on AlphaFold generated pdb files. It only outputs the header, without any secondary structure assignment. Please find a sample AlphaFold generated pdb file and the output via the links.

While the command is not working, it also doesn't throw any error that I could dig into. Any help to resolve this, and to generate DSSP outputs on AlphaFold structures will be extremely helpful. Thank you!

[mhekkel]

Hi, Are you trying to feed a PDF file to dssp? That's not going to work. PDB files, or better, mmCIF files are the way to go. And please, if you want to share files, use github by attaching your files to a message. I don't do google drive. regards, -maarten Op 14-10-2021 om 15:40 schreef Sumaiya Iqbal:

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Hi - I have a DSSP set up in my Mac which works perfectly. This is the command I use: |mkdssp 1mot.pdb -o 1mot.dssp| But that same command is not generating any SS assignment on AlphaFold generated pdf files. *It only outputs the header, without any secondary structure assignment*. Please find a sample AlphaFold generated pdf file <https://drive.google.com/file/d/1Qv9InycHX2VR5JxpT6vq9oav_XLI07K6/view?usp=sharing> and the output <https://drive.google.com/file/d/1c7C_CCt4nh9Oa4W4mRy6_gJlGhgAJ7th/view?usp=sharing> via the links. While the command is not working, it also doesn't throw any error that I could dig into. Any help to resolve this, and to generate DSSP outputs on AlphaFold structures will be extremely helpful. Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#28>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADNA47EHTDHPRRCSVKVTYXDUG3MVFANCNFSM5F7WFZTQ>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Maarten L. Hekkelman http://www.hekkelman.com/

[iqbals]

@mhekkel Apologies for the typo: I tried with pdb files, of course, not PDF. I'll be sharing the files in a moment.

Sumaiya

[iqbals]

Actually, I don't see any option to attach files with the massage here. I can only add a link. Would a dropbox link work for you, or maybe I can email you? @mhekkel

[iqbals]

@mhekkel Ok, I now tried with mmCIF file, and got this error (please see below), possibly hinting what is the issue.

When validating _database_2.database_id: Value 'AF' is not in the list of allowed values

Then I looked into the mmCIF file for AlphaFold structure and found these lines.

_database_2.database_code AF-O95292-F1
_database_2.database_id AF

Is there any way to have DSSP working with this database_id value?
Thanks,

[iqbals]

UPDATE: Adding the following line in place of the header of PDB solved the issue.

CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1

Thanks, nonetheless!