The home page allows the user to input details of a variant and request analysis of this by Missense3D-TM. There are two main ways in which to specify the query variant:

1. Please select the button marked "Position on 3D Structure" to input a variant as a residue position on a 3-d structure file. This input page requires knowledge of the position of the residue of interest onto the 3D coordinate file (residue numbering in 3D structures does not always match the residue numbering of the primary amino acid sequence). You can upload your own experimental or model structure (including AlphaFold models).
2. Select the button marked "Position on Protein Sequence" to input a variant as a position within a Uniprot sequence. The Input requires the protein UniProt ID, amino acid position, substitution and the PDB ID of the experimental 3D structure. You cannot upload your own structure here.

The Waiting Page is displayed when your request has been submitted and the variant is being analysed.

The page shows the time that your processing job was started. Please bear in mind that larger structures will take longer to analyse. When analysis is complete the display will automatically show the summary results page which will display a high-level summary of your results and a link to the detailed results page.

There is no user input required for this page.

The summary results page is displayed once analysis of the variant structure is completed and an overall prediction is available.

1. You can return to the home page by clicking on the link shown at the top of summary results page.
2. You can choose to download a copy of your results by selecting the "Download" button just below the link.
3. The summary results line gives a summary of the analysis results which includes the uniprot id and the name of the structure file processed. These link to the corresponding Uniprot page and PDBe pages respectively (where appropriate).
4. On the same line is confirmation of the variant position and the wild type and variant residue followed by a summary of any criteria which identfied likely pathogenic damage to the structure, each damaging criteria being shown in white text on a red background.
5. Finally, at the end of the summary line is a button marked "View Details" which will open the detailed results page in a new tab.

The Detailed Results Page is opened in a new tab in your browser.

1. You can choose to download a copy of your results by selecting the "Download" button near the top of the page.
2. Below this, on the left side of the screen is an area which is used to display an interactive model of the 3-d protein structure (this is highlighted by a red border in the image below). The structure can be rotated and zoomed interactively by using the mouse.
3. To the right of this area is a summary of the variant information and a panel which offers coarse-grained control of the display. Advanced users can click on the 'console' link at the bottom of this panel to open up a console window for fine-grained control of the structure display.
4. Below this an area titled "Detailed Analysis". If any criteria have indicated a pathogenic prediction then they will listed in information boxes at the top of this area.
5. Criteria which did not indicate pathogenic effect are listed in information boxes below the others. The information boxes are expandable and contain more detailed information about the analysis results for that particular criterion.
6. Finally, near the bottom of the page is a button marked "Check H-Bond" which will show a popup window listing the h-bonds detected by the analysis for the wild type and variant structures.