[chimerax-users] How to get the average pTM scores from an Alphafold multimer prediction

[Chen, Henry]

Is there a way to get the average all the pLDDT values for the entire complex? Isn't that how the program generates its ranking?

Thanks so much,
Henry

-----Original Message-----
From: Elaine Meng <meng at cgl.ucsf.edu> 
Sent: Wednesday, January 4, 2023 11:40 AM
To: Chen, Henry <hchen38 at illinois.edu>
Cc: chimerax-users at cgl.ucsf.edu
Subject: Re: [chimerax-users] How to get the average pTM scores from an Alphafold multimer prediction

Hi Henry,
The per-residue scores in the PDB file are pLDDT values, not pTM.  I don't know if pTM is included in the information that ChimeraX gets. As described in the help links below, ChimeraX shows pLDDT and PAE (predicted aligned error):

<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html*coloring__;Iw!!DZ3fjg!9Sn5HbsUfAGjOX6KCO4gTgqW8U-8KWx9hRu66Chltsb4p3nPBkXpVc9YKjWrZw7S6ZsdmYP3WbZvxLMCzXwS$ > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html*pae__;Iw!!DZ3fjg!9Sn5HbsUfAGjOX6KCO4gTgqW8U-8KWx9hRu66Chltsb4p3nPBkXpVc9YKjWrZw7S6ZsdmYP3WbZvxM3PnVJa$ >

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 4, 2023, at 8:27 AM, Chen, Henry via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear Chimarax devs/users,
>  
> I’m using ChimeraX Alphafold tool to do a multimer structure prediction. I was wondering how can I determine the average pTM score for each structure prediction? I get PAE.png and plddt.png file, but not a text file or anything that tells me the average pTM. (I was hoping the ranking file would give the average score but it does not) The models come with the pdb file as well as the scores.json files, but again I don’t see anything that tells me the average pTM for the structure. Clearly the pTM per residue scores are saved in my pdb file, is there a command to average them all up?
>  
> Thanks!
> Henry