Moloc Update History

Moloc carries a date, shown in the window title and as header of the main menu. Changes mentioned here are effective if they are older than your Moloc.

DateMenu-OptionDescription of Change
180203geo/w/g Msrfvl -g The quantity Vr (rotational volume) has been replaced by the more intuitive quantity Ve (extension volume) which is just the product of the three principal rms-extensions.
180120geo/w/g A (optional) graphical representation of the second-moment tensor has been added, which displays the three principal axes extensions.
171027mch/s/r This new option allows to print a rmsd table of the fragment atoms in the various entries.
171027mch/m/q This new option allows to print the rmsd of the specified atoms.
170929Moloc Finally, a way has been found to make mouse-driven view adjustment also working in Windows 10!
170821Mcnf 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).
170821Mdfy 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'.
170821cnf/c/a For the ring-shape algorithm automatic assignment of the ring is performed. The largest non-bridged ring of rhe structure is identified.
170821dYn/i/o This additional option to interactive docking performs a search with varying initial orientation of the ligand.
170803dYn/i 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 constrained).
170711nxr/e When generating crystal environments, Moloc generated duplicate copies (superimposed) in certain cases. This has been corrected. BUG
170702.../g 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 been supplemented.
161103Mcnf 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).
161103Mol3d Chiral constraints were not applied correctly in all cases. This has been mended. BUG
160920pca/c 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
160916MAB Structures with multiple rings could temporarily not be treated. The calculation stoped (Arngs failed!). This has been mended. BUG
160705xry/r/u Structure update did not work any more, owing to the generalization of the data structure (see 160217). This has been mended. BUG
160617.../i 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.).
160617Moloc 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.
160603Gr2d When writing a postscript file, labeling of curves was not transferred to the file. This has been added now.
160523Moloc 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.
160516Beginners Corner An additional section 'Key Control' has been introduced to explain the procedures of operating the various functionalities by key strokes.
160514Moloc 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.
160421Map Several equally spaced contours can be generated at once now.
160330frg/m 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 augmented correspondingly.
160308.../e/w 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.
160217Mdfy -p 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.).
160217.../g/b 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.
160217pca/e Parts of a structure (polymer chains or heterogens) can be extracted from an entry.
160122pca/p/d Heterogen components in a polymeric entry can be removed."
160111Alt B 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).
151221Map/k 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.
151216pca/k 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).
151213Dyn/h When driving torsions interactively, prepositionning (option 's') did not work properly. This has been mended.
151104.../a 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 display.
151104Mphmch This (seldomly used) batch program had bugs and worked rather slow. This has been mended.
150609.../g/i 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.
150609srf/c When calculating sufaces, the program crashed under certain conditions. This has been mended. BUG
150320pca/c/h... Rewinding files did not work properly in Unix (Linux) systems. This has been mended. BUG