[chimerax-users] Export pLDDT scores

[Tom Goddard]

Hi Asmahan,

  The pLDDT scores for an AlphaFold prediction are in the bfactor column of the PDB atomic model file.  Here is an example of lines from such a file where the value 85.53 is the pLDDT for residue 1.

ATOM      1  N   ASP B   1      -0.818 -36.026 -12.912  1.00 85.53           N  
ATOM      2  CA  ASP B   1       0.545 -35.783 -13.373  1.00 85.53           C  
ATOM      3  C   ASP B   1       0.706 -34.352 -13.882  1.00 85.53           C  

The bfactor is assigned to every atom.  But pLDDT is only assigned for each residue and measures CA position so you might want to look at only the CA lines.

$ grep CA ~/Downloads/ChimeraX/AlphaFold/prediction_14/af252_unrelaxed_rank_1_model_2.pdb
ATOM      2  CA  ASP B   1       0.545 -35.783 -13.373  1.00 85.53           C  
ATOM     10  CA  CYS B   2       1.983 -32.130 -13.721  1.00 95.45           C  
ATOM     16  CA  PRO B   3       3.029 -30.770 -17.151  1.00 93.20           C  
ATOM     23  CA  SER B   4       6.629 -31.094 -18.066  1.00 93.36           C  

You can also write the values into a ChimeraX attribute file using ChimeraX commands

	select #1 at CA
	save ~/Desktop/plddt.defattr attrName bfactor models #1 selectedOnly true

and that file looks like the following

attribute: bfactor
recipient: atoms
match mode: 1-to-1
	/A:1 at CA	56.150001525878906
	/A:2 at CA	53.33000183105469
	/A:3 at CA	53.59000015258789
	/A:4 at CA	59.380001068115234

documentation here

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#attributes

  Tom


> On Nov 22, 2022, at 7:08 AM, Asmahan Alghamdi <Asmahan.Alghamdi at nottingham.ac.uk> wrote:
> 
> Dear Tom, 
> I hope you are well. I was wondering if there is away to export pLDDT scores of the best predicted model of a protein using ChimeraX e.g. 1.5 (which I am using in my investigations)?  
> 
> Thank you very much.
> Asmahan 

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