Mario Valle Web

STM4 — open problems

Here are open problems with the current STM4 release. I hope to clean the list soon, but in the meantime please send me problems you eventually find. Thanks!

Problem list

  1. Apply Symmetries seems not to work with some symmetries (like P -6 for BN.res)
  2. Apply Symmetries does not work anymore after an "Illegal lattice translation (3)" message.
  3. After replicating a structure with fragment names and select fragment labels on fragments, the labels are crowded in the center of the structure.
  4. DCD reader: the file bucky.dcd shows an out of range value
  5. ComputeSelectedBonds needs a reset all button, plus seems the bonds are computed in a strange way


  1. Strange overlapping atoms in gulp examples 12, 19 and 20. Idem for Shel-X Fajausite
  2. Compute Selected Bonds needs to be activated by a small change to max dist slider
  3. Strange symmetry for nixquam_tri_p1.res. The original unit is outside the unit cell
  4. Verify if the limitation of data len equal 1 or 3 is justified
  5. PDB count frames: skip a frame if it has no ATOM or HETATM lines
  6. When replicating or selecting do not copy verbatim the fragment table
  7. The Draw Polyhedra module is difficult to use. It is missing a function to clear all polyhedra

Not really problems

  1. Should Move Structure rotate also associated vector data?
  2. The CIF reader needs a way to choose between multiple ways to describe symmetry
  3. Surface transparency in POV-Ray: not every surface!
  4. WritePOVray: add tetrahedra, add array of molecules
  5. Miller Plane: the scale values sometime (case nn0) enlarge the plane both directions, otherwise they enlarge them one side only
  6. Miller Plane: remove dependency from AVS vector macros