|Date||Menu-Option||Description of Change
|180203||geo/w/g Msrfvl -g||
The quantity Vr (rotational volume) has been replaced by the more intuitive
quantity Ve (extension volume) which is just the product of the three
A (optional) graphical representation of the second-moment tensor has
been added, which displays the three principal axes extensions.
This new option allows to print a rmsd table of the fragment atoms
in the various entries.
This new option allows to print the rmsd of the specified atoms.
Finally, a way has been found to make mouse-driven view adjustment also
working in Windows 10!
The batch-version of Moloc's conformation analysis has been augmented
by adding the ring-shape algorithm, which was previously only available
in interactive mode. Assignment of the ring is automatized (see cnf/c/a).
A new option, -tn, allows to modify a library of structures by
searching the largest non-bridged ring, followed by trimming the ring's
substituents to a maximum length of 'n'.
For the ring-shape algorithm automatic assignment of the ring is
performed. The largest non-bridged ring of rhe structure is identified.
This additional option to interactive docking performs a search with
varying initial orientation of the ligand.
This new utility allows to dock a ligand interactively to a receptor
by moving the ligand by hand. At any point a minimization of the
energy can be performend, either by repositioning or by full
minimization (optionally keeping internal degrees of freedom
When generating crystal environments, Moloc generated duplicate
copies (superimposed) in certain cases. This has been corrected. BUG
When reading files with multiple entries Moloc asks for a library
name for these entries. This did not work in all cases and has now
This program has been updated with respect to chiral constraints
(see previous entry). Furthermore, specification of chiral centers
(option -c) can now also be made by atom parity (.sd files).
The parameter -q (quick) has been extended to also allow for adding
(missing) Hydrogens. In addition, one can specify the maximum number
of conformations kept (parameter -k).
Chiral constraints were not applied correctly in all cases.
This has been mended. BUG
After a modification in the structure of C-alfa files, old files
were incorrectly read (Non-peptide bonds were not distinguished).
This has been mended. BUG
Structures with multiple rings could temporarily not be treated.
The calculation stoped (Arngs failed!). This has been mended. BUG
Structure update did not work any more, owing to the generalization
of the data structure (see 160217). This has been mended. BUG
The letter of menu-item 'interface extras' has been changed from
formerly ':' then '[' to 'i'. The reason being that all menu items
should be selectable by a single key-stroke without any modifiers
(Shift, Alt, etc.).
Considering that nowadays laptops are most frequently used, the
assignment of view-manipulation keys has been altered such that
they are restricted to keypad- and arrow keys which seem to be
least susceptible to keyboard design changes.
When writing a postscript file, labeling of curves was not
transferred to the file. This has been added now.
Key Control has been improved, in particular with respect to
forge-functionality, where switching between atom movement and
view adjustment is important. The corresponding section in the
'Beginners Corner' tutorial has been updated.
An additional section 'Key Control' has been introduced to explain
the procedures of operating the various functionalities by key
The program has been updated with respect to key-control
operation. This, with a view on running Moloc on Windows 8 (upwards)
where mouse-operation for third-party software is severely
restricted. The cause is the concept of mouse gestures in Windows
Aero, introduced in Windows 7, which apparently cannot be switched
off any more in later versions. For this reason all menu items
start now with a lower-case letter, for which some twenty menu
items had to be renamed. This is most evident in the main menue
where in a few instances the three menu-letters have been
rearranged somewhat artificially.
Several equally spaced contours can be generated at once now.
When producing movies with a set of moved atoms by keeping views
(Alt v), it is now possible to also adjust clipping planes in the
midst of the atom moving process. The help text has been
This new option allows to color bonds in a Calf-type structure
according to bond type, e.g. to emphasize S-S bonds in peptides
or H-bonded base-pairs in DNA/RNA structures.
This option has been removed, due to its limited usefulness. Moloc's
updated option .../g/b is a more complete replacement, which takes
care of the extended possibilities of mmcif, mostly larger numbers in
various structure properties (atoms, asymmetric id's, etc.).
Reading of mmcif files has been generalized. To cope with the
extended possibilities, the chain identifier (_asym_id) in Moloc
has been enlarged from a single character to a string. This led to
modifications in several places.
Parts of a structure (polymer chains or heterogens) can be extracted
from an entry.
Heterogen components in a polymeric entry can be removed."
A new toggle has been introduced which allows to switch to a
"drawn font". A drawn font displays characters by drawing lines
instead of displaying bitmaps in raster graphics. Some modern
graphics boards are very slow in in displaying bitmaps, because
this mode is hardly used in gaming applications. The startup
mode can be set in the .Moloc file by adding an additional
number in the "font" line (zero for bitmaps).
If several contours of a map are calculated one can now switch
between them by operating the mouse wheel. Only a single contour
may be visible at a time.
For DNA and RNA structures in reduced representation it is possible
to introduce additional bonds for H-bond bridged pairs.
This type of bond is not considered as connection in the definition
of sets (set menu).
When driving torsions interactively, prepositionning (option 's')
did not work properly. This has been mended.
For pharmacophore entries the active state newly influences the
mode of display. Excluded-volume agons are only shown with
markers instead of full meshed spheres. This avoids a crowded
This (seldomly used) batch program had bugs and worked
rather slow. This has been mended.
Reading .cif files from CSD resulted in crumpled structures,
because the space group could not be read. Reading space groups
from CSD files has now been added.
When calculating sufaces, the program crashed under certain
conditions. This has been mended. BUG
Rewinding files did not work properly in Unix (Linux) systems.
This has been mended. BUG