| Date | Menu-Option | Description of Change |
| 090724 | Msmab |
A new option, -w, allows to control the output of data fields for
energy and atomic charges to .sd files.
|
| 090724 | Mol3d |
A new option, -E, causes the program to write a data field
'MAB_ENERGIES', giving the values of MAB's various energy terms.
|
| 090707 | opt/e/h |
By choosing this option with the SHIFT key pressed one can now examine
repulsive energy contributions of the MAB force-field between pairs of
exclusive H-bond donors or pairs of exclusive H-bond acceptors.
|
| 090703 | pca/m |
A new utility has been implemented which allows for mutation of residues
in proteins or at protein interfaces. Tools allow to browse through
amino acids and rotamers and to evaluate and minimize energies. Surfaces
can be displayed for interactive visual examination.
|
| 090604 | MCA |
In the C-alpha force field, MCA, the 'valence angle' restoring
force has been increased. This avoids instabilities which occurred
in certain situations.
|
| 090517 | .../+/f |
This new option allows to split up an entry into separate entries,
one for each disconnected fragment.
|
| 090514 | Mcnf lib/t/m |
Specification of conformation constraints has been changed:
yes-no options '-t' and '-c' have been lumped together in a
numerical parameter '-c'. A value c=4 causes the program Mcnf
to apply the constraints given the input file.
|
| 090513 | Msmab |
A new option '-c' has been added. It causes the program to also
list conformational constraints in the output file.
|
| 090426 | expert corner |
The html page on Calf building has been augmented by a section
dealing with the particulars of handling non-natural amino-acid
residues.
|
| 090426 | pca/h |
This new menu allows to read in non-natural amino acids. They
are used when building up peptides containing such residues.
A host of utilities (mostly in 'pca' and Calf-building) have
been generalized to also handle these residues.
|
| 090326 | Msmab |
Enforcement of stereo specifications from SMILES was based on
an early, incomplete Daylight manual and could give false
results in structures with cycles. This has been corrected. BUG
|
| 090325 | Mol3d |
Enforcement of stereo specifications did not work properly.
This has been mended. BUG
|
| 081207 | lib/b/l |
This new switch allows to display label 'L', or data 'D'
(if available) of the current entry.
|
| 081004 | lib/e/y/l |
A leave-one-out test has been implemented in the regression
analysis utility.
|
| 081003 | lib/e/y |
For libraries, the entries of which have data associated with
them, regression analyses on these data can be performed.
Examination can be made by a graph or by browsing (see lib/b/a).
This new module is mainly used for method development within
Moloc, but it may be of general interest.
|
| 081003 | lib/b/a |
This new option allows to select entries of a library to be
browsed, by picking agons of a positions entry (see lib/e/v).
|
| 081003 | lib/e/v |
For libraries, the entries of which have data associated with
them, a positions entry can be generated, the agons of which
are associated with the entries of the library. The coordinates
of these entries are associated with the values of specified
data fields. Such data entries are also automatically produced
in certain places in Moloc. In the browse utility (lib/b)
entries can be selected by picking an agon of such a positions
entry.
|
| 080929 | .../g/o |
A new input parameter 'name-tag' can be defined. I causes the
program to take molecule-names from the corresponding tags in
a .sd file.
|
| 080914 | lib/f |
The element count option of the filter utility did not work
for some time now. This has been mended. BUG
|
| 080822 | MAB |
The table for bond radii has been updated.
This affects mainly some of the less common element.
|