Troubleshooting & Common Issues

This section addresses frequently encountered problems and provides solutions.

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Issue: Amino Acid Sequence Overlap/Jumbling

Problem

When the secondary structure diagram is quite long (i.e., for large proteins), the residue numbering and/or amino acid sequence often overlaps or becomes jumbled together, making it unreadable.

Solution

You can adjust the size of the residue numbers and sequence labels by changing the default font size. Use the --fontsize flag followed by a numerical value. The default size is 12, which may be too large for high-density diagrams. Try reducing it (e.g., --fontsize 8) until the text is clearly separated.

• Example: ssdraw single ... --fontsize 8

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Issue: Saving Secondary Structure to a Specific File Format

Problem

I need to save the generated secondary structure diagram in a high-quality vector format (like SVG or EPS) or a specific raster format (like TIFF) instead of the default PNG.

Solution

You can specify the desired output file type using the --output_file_type flag. This is particularly useful for generating publication-quality figures.

The supported output file types are: png, ps, eps, tif, and svg.

• To save as a vector graphic: ssdraw single ... --output_file_type svg
• To save as a high-resolution image: ssdraw single ... --output_file_type tif

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