Viewers

ProteinIQ's viewers let you inspect local scientific files without submitting a hosted analysis. Open them from Viewers in the sidebar. Viewing a file does not create a job or save it to your workspace library.

PDB Viewer

PDB Viewer displays molecular coordinates in an interactive 3D scene. It accepts PDB, mmCIF, SDF, MOL, MOL2, PDBQT, XYZ, and GRO files.

Select Click to upload or drop supported files onto the upload area. You can select several files to load them into the same scene. Open blank PDB viewer opens the viewer without an initial file.

Rotate and zoom the scene to inspect the structure. Use the sequence and structure controls to locate chains or residues and adjust the representation. Loading two structures into one scene does not by itself establish that they have been structurally aligned.

The camera control opens image capture options. Use Download in that panel to save an image of the view. Keep the coordinate file as well; an image cannot replace the molecular data needed for another analysis.

Local files are read in the browser. The viewer needs WebGL to render the scene. If it does not load, check the displayed error, file contents, and browser graphics support.

MSA Viewer

MSA Viewer displays an existing multiple sequence alignment. Supported formats include aligned FASTA, CLUSTAL, Stockholm, PHYLIP, and MSF.

Select Click to upload or drop an alignment file onto the upload area. The viewer detects its format and displays the aligned residues. It does not align unaligned sequences; create an alignment with an appropriate tool first.

Use the coloring, sorting, and display controls to inspect the alignment, consensus, and conservation. Check whether filters are active before interpreting the visible rows or positions.

Open the export control for Export alignment. Choose the scope and available image format in the dialog. Some export formats depend on your plan. The separate FASTA action applies the current sequence search, ordering, and column filtering; the image scope selector does not change it. Keep the original alignment separately.

Molecule Drawer

Molecule Drawer is a chemical structure editor. Draw a molecule on the canvas or import a supported representation, such as SMILES, MOL, SDF, InChI, or KET.

To try a small example:

1. Enter CCO in the Import text area.
2. Select Import to load the molecule.
3. Inspect or edit the structure on the canvas.
4. Select an Export format and choose Export.

The export downloads the selected representation. Available choices include SMILES, MOL, SDF, InChI, InChIKey, KET, SVG, and PNG. Text exports also appear in the output area. SVG and PNG preserve the drawing; use a chemical representation when another tool needs molecular data.

Check stereochemistry, charge, and the destination tool's requirements before using an edited molecule. Exporting a drawing is not a guarantee that it has the three-dimensional geometry or preparation required for a calculation.

Continue an analysis

To keep a local file in your workspace, upload it to Files. From there, Send to tool lists compatible destinations and lets you review the input assignment. A viewer's local file state is separate from saved files and job results.

Tool result panels can also include structure and alignment viewers. Available controls depend on that output. Use the tool's documentation for the meaning of its measurements and the input preparation guide when preparing data for another run.