updated docs: Interpreting PoET Results Table

Author: d2phap

source/_static/tools/poet/results-table-expanded.png

@@ -8,9 +8,9 @@ This tutorial explains how to interpret the results generated by the PoET Genera
 Results Table
 ^^^^^^^^^^^^^^
 
-Your results are presented in a table, with each generated sequence assigned a log-likelihood score. This score reflects how well the generated sequence fits the prompt: a higher score indicates a better fit.
+Your results are presented in a table, with each generated sequence assigned a log-likelihood score and other metrics, such as Identity, pLDDT, RMSD, TM Score, depending on the selected Alignment Method. You can customize the displayed columns using the right-click menu from the table header.
 
-Right-click any sequence to access local fitness landscapes through the **Run Substitution Analysis** menu. You can also sort your results and export them using the **Export** button.
+Right-click any sequence to access local fitness landscapes through the **Run Substitution Analysis** menu. You can also sort, filter your results and save them to file using the **Export** button.
 
 .. image:: ../../_static/tools/poet/results-table.png
    :alt: Results Table
@@ -21,16 +21,34 @@ Structure Prediction and Comparison
 
 Once the structure prediction job completes, the structure viewer will appear on the right side of the page. The prediction model can be changed via the **Structure Predictor** dropdown located above the viewer. Hover over a sequence in the results table to preview and compare its structure against the query structure. The viewer also displays key metrics, including:
 
-- **pLDDT (predicted Local Distance Difference Test)**: A per-residue confidence score (commonly scaled from 0-100 or 0.0-1.0) indicating how reliable each residue's predicted position is.
+- **Log-likelihood score**: Reflects how well the generated sequence fits the prompt. A higher score indicates a better fit.
+
+- **Identity**: The percentage of matching amino acids between the generated sequence and the reference across the aligned region.
+
+- **pLDDT (predicted Local Distance Difference Test)**: A per-residue confidence score (commonly scaled from 0-100) indicating how reliable each residue's predicted position is.
 
 - **RMSD (Root Mean Square Deviation)**: A measure of structural similarity between two molecules, typically comparing backbone atoms. Lower RMSD values indicate greater structural similarity.
 
+- **TM Score (Template Modeling score)**: A measure of the similarity between two protein structures. Higher means more similar.
+
 Click a sequence to expand the structure viewer, which will overlay the results table. In this view, you can examine detailed metrics and sequence-to-prompt alignment for the selected sequence.
 
 .. image:: ../../_static/tools/poet/results-table-expanded.png
    :alt: Sequence structure viewer
 
 
+Change Alignment Method
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The alignment method used for structural comparisons can be changed via the **Alignment Method** toggle buttons located above the results table. Available methods may include:
+
+- **Structure**: Structures are superimposed with TM-Align algorithm, and this superposition is used to compute structure similarity metrics, such as RMSD and TM Score.
+
+- **Sequence**: Sequences are aligned with Needleman-Wunsch algorithm, and then structures are superimposed via Kabsch algorithm using the sequence alignment. This superposition is then used to compute structure similarity metrics.
+
+- **Off**: Sequences are aligned with Needleman-Wunsch algorithm if they are same length as the prompt; otherwise, no alignment is performed, some metrics such as Identity, RMSD and TM Score are not available.
+
+
 Change Reference Structure
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^