Help in Extracting pLDDT confidence Scores in CSV Format from ChimeraX AlphaFold
Dear ChimeraX Developer, I hope this message finds you well. I am reaching out as a newcomer to ChimeraX and Alphafold, seeking guidance on extracting the pLDDT score in CSV format from the best model obtained through ChimeraX AlphaFold.
Specifically, I am interested in obtaining information such as Binding Protein, Bond Type, Protein Residue, Peptide Residue, Distance (Å), and the "pLDDT Range Score." Despite my attempts with the B-factor, I have encountered challenges in extracting the pLDDT range confidence score.
I would greatly appreciate any assistance or guidance you can provide on this matter.
Thank you for your time and consideration.
Kind regards,
Amit
Hi Amit, If you just save a PDB file of the model (or if you got a PDB file from AlphaFold database in the first place), you can just look in in the PDB file ATOM records with a text editor. These files have the pLDDT value where the B-factor would normally be. See description of PDB file format:
For example, ChimeraX commands:
open apoe_human from alphafold save test.pdb
...then looking in test.pdb, I can see that the ATOM lines for the first two residues show that the first residue has pLDDT 44.23, the second residue has pLDDT 43.65, ...
ATOM 1 N MET A 1 65.225 21.096 -17.172 1.00 44.23 N ATOM 2 CA MET A 1 64.291 22.233 -17.358 1.00 44.23 C ATOM 3 C MET A 1 62.878 21.847 -17.825 1.00 44.23 C ATOM 4 CB MET A 1 64.903 23.319 -18.255 1.00 44.23 C ATOM 5 O MET A 1 61.953 22.574 -17.502 1.00 44.23 O ATOM 6 CG MET A 1 66.149 23.956 -17.624 1.00 44.23 C ATOM 7 SD MET A 1 65.853 24.683 -15.993 1.00 44.23 S ATOM 8 CE MET A 1 66.622 26.313 -16.237 1.00 44.23 C ATOM 9 N LYS A 2 62.654 20.725 -18.536 1.00 43.65 N ATOM 10 CA LYS A 2 61.321 20.343 -19.069 1.00 43.65 C [etc.]
As for CSV, as far as I know you would need to write your own script to generate that format and get the other pieces of information you mentioned. You can see residue name in the above, but other information would need to come from measurements or looking at other part(s) of the output files, or your own prior knowledge.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2024, at 11:59 AM, Amit Singh via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX Developer, I hope this message finds you well. I am reaching out as a newcomer to ChimeraX and Alphafold, seeking guidance on extracting the pLDDT score in CSV format from the best model obtained through ChimeraX AlphaFold.
Specifically, I am interested in obtaining information such as Binding Protein, Bond Type, Protein Residue, Peptide Residue, Distance (Å), and the "pLDDT Range Score." Despite my attempts with the B-factor, I have encountered challenges in extracting the pLDDT range confidence score.
I would greatly appreciate any assistance or guidance you can provide on this matter.
Thank you for your time and consideration.
Kind regards,
Amit
Sorry, forgot to add the links for PDB file format. See the following, where "Temperature factor" is the same thing as B-factor:
https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.html#coords https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
On Jan 14, 2024, at 2:18 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Amit, If you just save a PDB file of the model (or if you got a PDB file from AlphaFold database in the first place), you can just look in in the PDB file ATOM records with a text editor. These files have the pLDDT value where the B-factor would normally be. See description of PDB file format:
For example, ChimeraX commands:
open apoe_human from alphafold save test.pdb
...then looking in test.pdb, I can see that the ATOM lines for the first two residues show that the first residue has pLDDT 44.23, the second residue has pLDDT 43.65, ...
ATOM 1 N MET A 1 65.225 21.096 -17.172 1.00 44.23 N ATOM 2 CA MET A 1 64.291 22.233 -17.358 1.00 44.23 C ATOM 3 C MET A 1 62.878 21.847 -17.825 1.00 44.23 C ATOM 4 CB MET A 1 64.903 23.319 -18.255 1.00 44.23 C ATOM 5 O MET A 1 61.953 22.574 -17.502 1.00 44.23 O ATOM 6 CG MET A 1 66.149 23.956 -17.624 1.00 44.23 C ATOM 7 SD MET A 1 65.853 24.683 -15.993 1.00 44.23 S ATOM 8 CE MET A 1 66.622 26.313 -16.237 1.00 44.23 C ATOM 9 N LYS A 2 62.654 20.725 -18.536 1.00 43.65 N ATOM 10 CA LYS A 2 61.321 20.343 -19.069 1.00 43.65 C [etc.]
As for CSV, as far as I know you would need to write your own script to generate that format and get the other pieces of information you mentioned. You can see residue name in the above, but other information would need to come from measurements or looking at other part(s) of the output files, or your own prior knowledge.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2024, at 11:59 AM, Amit Singh via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX Developer, I hope this message finds you well. I am reaching out as a newcomer to ChimeraX and Alphafold, seeking guidance on extracting the pLDDT score in CSV format from the best model obtained through ChimeraX AlphaFold.
Specifically, I am interested in obtaining information such as Binding Protein, Bond Type, Protein Residue, Peptide Residue, Distance (Å), and the "pLDDT Range Score." Despite my attempts with the B-factor, I have encountered challenges in extracting the pLDDT range confidence score.
I would greatly appreciate any assistance or guidance you can provide on this matter.
Thank you for your time and consideration.
Kind regards,
Amit
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participants (2)
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Amit Singh -
Elaine Meng