Known Bugs and Limitations

1. Error messages are not properly reported when invalid commands are entered into the NMR Model Script box. This will be fixed before version 1 is released.
2. Chime 2 beta 1 for Macintosh lacks a version detection mechanism so will not be properly detected. This problem has been reported. Results are untested.
3. Chime 2 beta 4 for Windows, when in multiple model (NMR) mode, cannot execute a script file. It can execute script commands typed into the command line slot, but not scripts stored in disk files. This bug has been reported.
4. Chime 1 does not support NMR models -- it will show the first model only. This limitation has been removed in Chime 2.
5. Chime 2 does not report the number of NMR models loaded so the default number of 50 must be set to the actual number manually. The actual number of models can be found by examining the remarks in the PDB file. (Open it in a text viewer such as Wordpad or Word). This limitation has been reported.
6. Chime 1 on Macintosh has a bug which prevents any mouse clicks on the molecular graphic from working, e.g. identifying the atom clicked, reporting distances or angles, etc.

Version History

• October 18, 1998: beta-test version 0.92.
  • A slot has been provided which allows the user to specify script commands for any desired representation and color scheme for displaying NMR models. In the Protein Comparator, separate scripts can be specified for each molecule (top vs. bottom).
  • A number of minor bugs were fixed, and minor conveniences added, including a [Del] button to delete unwanted entries from the "Previously loaded PDB file" pick list.
  • Some non-obvious design features were documented, and information is provided about PE's use of cookies.
• October 7, 1998: beta-test version 0.91.
  • The Macintosh does not allow PDB ID codes to be typed into the Browse slot. Therefore a separate slot has been provided for PDB ID's.
  • A bug which prevented items on the menu "Select previously loaded PDB file" from loading correctly on Macintoshes has (we hope) been fixed.
  • Water button now toggles water between hidden, dots, and spacefill. Bugs fixed: hetero button and water button now work in Comparator.
  • A bug which prevented the built-in Protein:DNA from being reported by the [?] button which reports "last file loaded" has been fixed.

• October 4-5, 1998: beta-test version 0.9.
  • This is the first beta-test version, not yet an officially released version. It was offered to subscribers to the on October 4. On October 5, a bug in file-loading via Browse was fixed.

This section lists design features which may not be obvious when using the Protein Explorer.

• The Protein Explorer (PE) requires cookies.
• When the client is using Chime 2, PE communicates with Chime via LiveConnect. When the client is using Chime 1, PE communicates with Chime via the immediate-mode button mechanism (button in an invisible dummy frame).
• When PDB files are obtained directly from a PDB mirror site via Internet, PE uses a URL at the PDB which transmits the PDB file in gzipped form. This typically reduces transfer time by nearly four-fold.