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!