PTGLweb -- Help

Biomedical examples
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If you need help using the website or interpreting the results, do not hesitate to contact us.

Linking PTGLweb
The PTGLweb REST API
Frequently Asked Questions

Linking PTGLweb

You can link PTGLweb in several ways, depending on the kind of data you want:

Link to all protein graphs of a chain:

Format: http://ptgl.uni-frankfurt.de/results.php?q=<pdbid><chain>
The allowed values for the parameters are:

<pdbid>: a PDB identifier
<chain>: a PDB chain name

Example for PDB 7tim, chain A: http://ptgl.uni-frankfurt.de/results.php?q=7timA

Link to all folding graph linear notations of a protein graph:

Format: http://ptgl.uni-frankfurt.de/foldinggraphs.php?pdbchain=<pdbid><chain>&graphtype_int=<graphtype_code>&notationtype=<notation>
The allowed values for the parameters are:

<pdbid>: a PDB identifier
<chain>: a PDB chain name
<graphtype_code>: 1=alpha, 2=beta, 3=albe, 4=alphalig, 5=betalig, 6=albelig
<notation>: a notaion: adj, red, seq or key

Example for the ADJ notation folding graphs of the alpha protein graph of PDB 7tim chain A: http://ptgl.uni-frankfurt.defoldinggraphs.php?pdbchain=7timA&graphtype_int=1&notationtype=adj

The PTGLweb REST API

We are offering a REST API for programmers. Please see the API documentation for details.

Frequently Asked Questions (FAQs)

Why is there no result for my PDB ID?

Check that the entered PDB ID (4 characters) is correct.
PTGL is currently updated annually, check that the structure is not too new. You can find the date of the last update here (content).
Structures with a resolution worse than 4.5 Angstroem are excluded.
Structures containing less than 30 residues are excluded.

What can I do about it?

You can compute your own results with the open source PTGLtools software.

Why is there no graph image?

PTGL is optimized to process large structures. In rare cases, images of secondary structure element-level Complex Graphs may be missing (PNG and SVG files). This can be the case for really large structures, when their size gets too enormous for most browsers and applications to handle. For example, the secondary structure element-level Complex Graph of 3j3q would have a width 832,256 and a height of 208,512 pixels.

Check that the graph image really is missing. Because of the image size in these extreme cases the image may need some time to load. Most browsers show a sign that they are still loading data.
If your browser fails to load the image, but the download button exists, you can download and view it manually with an image viewer of your choice.