Amyloid Atlas Illustrator

input file: Supply coordintes in .pdb format; this server does not handle mmcif format. Important Information
  1. Atoms missing from any residue will cause the job to crash. Build in any missing atoms or delete the residue completely (e.g. use COOT).
  2. If you are submitting a structure determined by NMR, submit only a single model of interest. Multiple MODELs (e.g. PDB ID 2beg) will produce errors.
  3. Include coordinates for at least three layers of the amyloid fibril. We regard a "layer" as a slice of the fibril perpendicular to the fibril axis. More specifically, one layer includes all atoms in the asymmetric unit of the fibril assuming C1 helical symmetry. It is important to include multiple layers to get an accurate estimate of the energetic stability of the fibril. Our method of evaluating energetic stability depends on measuring surface area buried by the fibril assembly. If you supply only one layer, the energetic stability of the fibril will be greatly underestimated. Note that most amyloid fibril models deposited in the PDB have at least 3 layers, and so work fine with this server. The server will report the energy for the layer most buried in the fibril.
  4. The coordinate file should contain no more than 9000 atoms, otherwise the job will crash.
  5. No two atoms in the .pdb file should share the same chain ID and residue number, as is usual and customary.
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rotx (rotation X): rotx is typically set to either 0 or 180 degrees, corresponding to views of the fibril from either the +z or -z directions. More information
  1. Any value from -180 to +180 is allowable, but in most cases, 0 or 180 are the most informative. It is standard for the fibril axis to be oriented parallel to the "z" axis in coordinate files determined by CryoEM, but not for NMR structures. The orientation of the fibril axis does not effect the energetic evaluation, but it will change the perspective of the fibril rendered in the output figure. If the perspective in the figure looks strange (i.e. small and overly crowded with atoms), check whether the fibril axis is parallel to "z". If not, use a program such as COOT to reorient the fibril axis to be parallel with "z" and submit the reoriented coordinates.
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ROTz (rotation Z)

rotz is can have any value (-360 to +360). It adjusts the orientation of the fibril in the plane of the screen.

PH value

The pH value given here will affect the charge assigned to ionizable residues. The ionization state will affect the atomic solvation parameter assigned to an atom, and thus its energy.
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