VMD 1.8.6 Bugs, Limitations, and Workarounds

Alas, there are still bugs and inconsistancies in VMD. Following is a list of known problems, limitations, and workarounds. For any issues not specifically listed here, please be sure to check the VMD release notes.

General

  • VMD will not draw ribbon or cartoon representations of cyclic proteins Update 3/2007: A test version of VMD is now available which can correctly draw cyclic proteins. Until the new code is fully tested it will remain an experimental feature, but we are happy to provide it on request.
  • VMD will not draw ribbon or cartoon representations of polysaccharide or carbohydrate chains. Update 1/2007: We are working on new carbohydrate-specific representations which will become available in a future version of VMD. If you're interested in testing the new carbohydrate rendering code, we can provide it on request.
  • An incorrect PDB accession code or download failure causes a 0 atom molecule to be loaded, though error messages are printed to indicate the problem. Delete the extra molecule.
  • VMD contains a bug in the old "cartoon" representation, where there are sometimes gaps between tubes and beta sheets. Use the "NewCartoon" representation which doesn't have these problems.
  • The current version of the PDB plugin does not handle illegal/invalid CONECT records very well. If a PDB file contains CONECT records that reference invalid atom IDs, it treats the invalid atom ID as "0". If this occurs, you may see warnings about when loading files with such invalid CONECT records, which complain about bonding index 0 to itself. If you encounter this situation, it is best to tell VMD to ignore the PDB CONECT records and to find bonds only via it's automatic distance-based bond determination method. This can be done by loading the file through the text interface, with a command like this: "mol new badconectrecs.pdb filebonds off"
  • In at least one case on the Linux platform, it is possible to crash VMD by loading a CCP4 format CryoEM map, displaying the map with an Isosurface representation and changing the coloring mode to "Molecule". The crash has thus far only occured on Linux, and only when running with OpenGL enabled, so it may be a video driver related problem. We are currently working on determining the cause and resolution to this problem.

Microsoft Windows Specific

  • The Win32 versions of VMD do not include Python yet, for reasons explained here, and on the Python web site.
  • Some combinations of video drivers and window operations can cause VMD windows not to be redrawn properly when they are uncovered. (believed to be an FLTK bug with expose events generated by the Win32 text console window) We believe this problem will be solved once and for all when we replace the Win32 text console window with our own (based on TkCon, or FLTK).
  • The 'vmdmovie' plugin has problems compressing movies into directories with names containing spaces, due to a bug with the "VideoMach" program used to convert movies on Win32.

MacOS X Specific

  • Tk, and TkCon bugs: Users running MacOS X on Intel based Macs have reported several bugs that are attributed to the MacOS X version of Tk. The most serious of these is a situation where TkCon becomes unresponsive and stops responding to keystrokes. When this occurs, proper function can usually be restored by selecting another application window (not VMD), invoking the MacOS "expose" feature (press F9, or Fn-F9 on the keyboard), and selecting the TkCon window again. This will restore the keyboard focus to the TkCon window. Future versions of VMD will use a newer Tcl/Tk version that we hope will fix this problem.
  • The VMD PDB parser will not accept files with lines terminated by carriage return characters (a tendency of Mac text editing programs).
  • The Mac version of MSMS appears to misbehave when generating a surface for some molecular structures. Specifically, loading the PDB '1hzx' does not produce a surface on the Mac, though it works fine on other platforms. Note: This is not a VMD bug, but is noted here for reference.
  • The MacOS X version of STRIDE fails to compute the secondary structure for the system "1S5L" with the selection "protein".

Unix Specific

  • The AIX5 and AIX5_64 builds of VMD 1.8.6 may return an incorrect value for the percentage of memory free (e.g. -1 or a large negative value) at startup time. This is not harmful as the memory availability code is only used for informational purposes at the present time. This will be fixed in a future release.
  • Some SGI systems will return a stereo visual that only works with "above/below" stereo, which is not supported by VMD. In this case, VMD will incorrectly report that stereo is available, though it isn't really available.
  • The 64-bit SGI IRIX version of VMD includes a 'psfgen' plugin that crashes when used. This occurs when VMD and the psfgen plugin are compiled with certain versions of the SGI MIPSPro compilers. We are working on a resolution to this problem.