Noncovalent Bond Finder: Version History
- August 31, 2002: Version 1.52.
- A visitor meter was added to the bottom of the main page (index.htm)
on June 20, 2002.
- Minor changes were made to retain compatibility with
the current version of the "shared" support files
(killCookie ciao bug fixed; alias.js changed to alias0.js).
- June 26, 2000: Version 1.51.
At some point in time, NCBF's ability to
load PDB files from the Protein Data Bank or its mirrors
ceased to work due to upgrades to the shared file system
and/or the PDB mirrors. This has been fixed (I think).
- June 29, 1999: Version 1.5.
- A number of bugs which affect only Macintoshes were fixed.
The NCBF now appears to work well on Macintoshes with Chime 2.0a
either from our server or from locally installed NCBF files.
- The NCBF was made freely downloadable for local installation.
- Several bug fixes and some minor improvements were completed.
Messages are now better controlled. Atom identifications are now messaged
when clicking in "Show Residue: CPK Colors" mode. The target is automatically
centered when entering the Finder.
- Command aliases are now expanded. Click on Show Aliases underneath
the message box.
- Many shared files were moved to a separate folder named shared
to facilitate maintenance and reduce duplication with future versions of
other UMass Chime resources which may be downloaded.
- November 8, 1998: Version 1.44.
- Attempted to fix some problems with loading PDB files on the Macintosh,
pursuant to the full release of Chime 2 for the Macintosh.
- April 26, 1998: Version 1.43.
- The help on selecting target atoms has been greatly improved.
A completely new general introduction to the select command
in Chime and RasMol has been provided.
- Help windows are now resizable.
- April 24, 1998: Version 1.42.
- Documentation improvement: The "fun example" in the Instructions entitled
"Water bridges between MHC and peptide" was updated to reflect capabilities
added in version 1.41.
- Minor bug fixed: Water oxygens found prior to replacing the target
with a mouse click no longer turn red when clicked in Show residue:
CPK coloring mode (they remain magenta).
- April 22, 1998: Version 1.41.
The menu of previously loaded PDB files now survives between sessions
The starting radius can now be changed from 2.5 Angstroms simply
by editing the initial radius announcement in the form slot.
A slot has been provided to "Find only". For example, you can put
"hydrophobic" here and find only hydrophobic residues.
- A "Mouse clicks" option to "Hide residue bonds" has been added
for decluttering the view when too many residues have been shown
via mouse clicks.
button has been added. This may be useful after several find cycles
to visualize the total set of found atoms/residues, all colored by
chain, all found atoms with dot clouds.
A command-line slot has been
provided at the bottom of the finder; see the help button there.
- When "Mouse clicks" is used to replace or add to the target,
the finding radius is reset to 2.5 Angstroms (from which it can be
changed manually if desired).
- Restoring the original target no longer unconditionally resets
the finder (you can manually reset if you wish).
- When centering an atom, or the entire target, or replacing the
target with a mouse click, the image is now centered automatically,
(Formerly, you had to zoom manually.)
- A bug was fixed which caused hydrogens in found water to be
colored magenta (now they're CPK white).
was fixed which caused the message filter to fail to work.
border has been inserted between the right and left frames. This means
it can now be dragged; for example, you could widen Chime for a stereo view.
- This bug was fixed in Chime 2.0.
colors often change at random to white; this is due to a
bug in Chime
over which we have no control. (This bug has been reported.) Best
workaround is to simply press the Background button to restore the
desired background color.
The package now starts up by opening a new
(2nd) window; this precludes inadvertantly starting it in an existing
frame, which would cause problems.
- April 15, 1998: Version 1.3.
The default background color is now white, but this can be changed
with a new button which cycles it through gray, black, and white.
Previously loaded PDB files can now be recalled from a select menu.
Messages are now filtered: only atom identification messages and
manually typed commands are displayed in Chime's message window.
(Message filtering can be disabled with the Debug button.)
included in the target is now colored magenta instead of CPK red.
Monitors are no longer erased by the Find button.
Bonds are shown (as
sticks) for found atoms covalently bonded to the target. (Yes, the
finder uses only distance so it will find covalently bonded non-target
atoms, if present and not specified as "don't find".)
clicks (tho it is not a mouse click) there is a new option to center
the entire target. This is useful after a single atom has been
centered, to recenter the entire target.
Under mouse clicks, there are powerful new
options to add to or replace the target with the atom or residue
clicked. To counter these, there is a new option to restore the
- April 13, 1998: Version 1.2.
The major reason this package crashed Navigator so often seems to have been
identified and fixed! (Namely, we now use Liveconnect to send scripts to Chime
instead of the old dummy frame/immediate mode button method.)
There are now continually updated displays of the number of target atoms,
the number of atoms found in the most recent cycle, and the total number
of atoms found.
A mouse click option was added to change the center of rotation/zooming.
This avoids having to translate the image and then fighting with
the automatic zoom centering, when wishing to zoom in on something
near the edge of the target set.
The initial view now
shows hetero atoms in CPK colors instead of a single "chain" color
assigned to all hetero atoms.
Some select lists were changed to checkboxes or radio buttons.
This makes the selected options more obvious, and makes room for
additional options (to be implemented in the future).
A few typographical errors were fixed. Documentation was updated.
- April 9, 1998: Version 1.1.
A mode was added which shows the entire residue containing a found
atom when the found atom is clicked.
A new variant of the "Target spacefilled yellow/white" mode colors
the proximal target atoms by CPK, thereby identifying them.
A bug was fixed which often caused finds to fail when the distance was an
The distinction has been clarified between the distance for the
found/displayed atoms, and the distance for the next find cycle.
Several "Fun Example" tutorials have been added to the instruction help page.
Other minor corrections and cosmetic improvements were made.
- April 7, 1998: Version 1.0.