Known Unresolved Issues
in FirstGlance in Jmol
Planned Features (not yet implemented)

- Providing support for translations to Spanish and other languages.
- Providing a clickable sequence listing. This is not a trivial project (see Specifications).
- Displaying alternative sidechain positions. (Examples: 3OVO, 5HVP, 9INS.)
- Send your suggestions using the feedback link below.

Known Unresolved Issues

Problems in the Jmol Applet (Jmol through 10.00.48)
- See the separate list of Bugs in Jmol.
- Pushing two buttons or view links in rapid succession causes the second to be ignored. (Workarounds: wait a few seconds between clicks, or push the second one again.)
- Very large PDB files may fail to display ( More..). Even when displayed, view links in FirstGlance may not function properly (see SV40 capid example in the Technical Gallery).
- Non-standard residues sometimes fail to be detected; instead, their non-standard atoms display as ligand. This is unlikely to be fixed.
- Occasionally Jmol fails to deem certain standard amino acids as "protein". We have been able partially to compensate by specifically adding all twenty standard amino acid names to "protein". Thus, for example, residues 1-3 in 1AL4. display as protein in the Composition, Hydrophobic/Polar, and Charge displays. However, we are unable to get them to be included in backbone trace displays. Better than nothing, we have been able to show them as alpha-carbon spheres in backbone trace displays (e.g. in 1AL4). To avoid having some of these atoms be invisible in most views, FG deems them Anomalous Atoms, and shows them in FG's initial view as dots. Resolution of this problem is in progress. More.. See also Bugs.
- Occasionally Jmol fails to connect some atoms with covalent bonds, when it appears that those atoms should be connected. Dramatic examples are the TRP sidechains in the Vines.. display in 1AL4, and several amino acids in 2SOC. See also Bugs.
- A bug in Jmol reports THR918.N in 1H3O, incorrectly as oxygen in the hover report, and colors it as oxygen. More.. See also Bugs.
  Problems in the FirstGlance code.
- The top of new help panels is not visible when first displayed if the previous help panel was scrolled down. If you know how to force the text in a division back to the top, please enlighten us (feedback link below). On the other hand, when checkboxes are clicked in help documents with many such options (such as Contacts Shown), the document is rewritten on each click, and it is advantageous that it does not return to the top after each click.
- 4CPA, in the Gallery, contains both unnamed and named protein chains. This is probably illegal in the PDB format and is very rare (perhaps unique). It confuses the "click to select" interfaces in FG, such as Contacts.. and Hide... (Many PDB files contain a single unnamed chain. FG handles these by assuming that if a standard residue without a chain name is clicked, there is a single, unnamed chain.)

Please report any anomalous behavior not mentioned above to
Be sure to include the PDB code!