Alas, there are still bugs and "inconsistancies" in VMD. Following is a list of known problems and a description of how to work around them.
  • Changing the "Color Scale Method" in the color menu does not immediately affect surface renderings. Only surfaces created after the setting is changed are correctly colored.
  • Some Windows ME systems fail to work correctly with the Winzip self-extracting software installer code. Unzipping manually works perfectly.
  • An incorrect PDB accession code or download failure causes a 0 atom molecule to be loaded rather than for an error/info message to be printed.
  • The MacOS-X version of VMD does not have a normally functioning help button. This is a deficiency in our implementation of web-based help on the Mac, and we are looking to provide a better solution soon, but time constraints prevented us from solving this issue prior to the first release of containing the MacOS-X version.
  • The OpenGL versions of VMD use the standard GLX routines to ask for a visual that supports stereoscopic display. VMD then proceeds to use the standard GLX mechanisms for performing buffer swaps on the stereo visual. Some SGI systems will return a visual that supports a special form of stereo requiring special handling (i.e. the normal GLX calls have no effect). VMD does not presently contain the code necessary to support these systems.
  • There are a small number of rendering bugs in VMD related to the connections between tubes and beta sheets, and between tubes in the "cartoon" representation. These will be fixed in a future version of VMD. (there are tiny gaps between the end of tubes, sheets, or cartoons in some circumstances)
  • Changing some of the atom information (secondary structure classification, beta and occupancy values, etc.) doesn't update the graphics display automatically. Workaround: press the "Apply Changes" button on the graphics form.