VMD 1.9.1 Bugs, Limitations, and WorkaroundsAlas, 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.
- VMD will not draw ribbon or cartoon representations of cyclic proteins. 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.
- 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.
- When used on Windows or MacOS X, the "Every Residue" control in the Timeline plugin may appear as "very residu". This will be fixed in a subsequent plugin update and the next VMD release.
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".
- None at this time