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Updates 1999

Updates 1999

DateMenu-OptionDescription of Change
991222mch/d/5 An additional matching option by rooted topological pharmacophors has been added.
991222mdcmsrch The Medchem database has been rebuilt (version 99) and the seach script 'mdcmsrch' been updated to yield the top-hit files m400.tdt and m400.mab together with the full similarity file (see tpr-Databases in Basel).
991221acdsrch The Available-Chemicals database has been rebuilt and the seach script 'acdsrch' been updated to yield the top-hit files a400.tdt and a400.mab together with the full similarity file (see tpr-Databases in Basel).
991215nosrch A database "nosis" has been generated from the ROSIS structures wich are not available. The search script nosrch returns the top-hit files n400.tdt and n400.mab together with the full similarity file (see tpr-Databases in Basel).
991215pca/k Monomer structures can now also be generated from pure nucleic acid structures. At present they are solely ment for display purposes.
991208mch/d/0 The possibility of performing superimpositions by topological pharmacophore matching has been added.
991208rosrch The search script has been modified to rank according to the subpharmacophore type similarity measure (sort -nrk3). In addition, the script extracts the 3-dimensional structures of the 400 top-ranked molecules into a file called r400.mab.
991208Mabxtr A new option -d has been introduced to allow to specify a common path for the set of .mab files.
991207Mabxtr This auxillary program allows to extract the coordinates of a list of structures from a set of .mab files (useful after ROSIS database searches).
991203srf/d/s
srf/d/b
The set of atoms leading to a surface can be regenerated (s). The previous option s (stitch) has been renamed to b (beautify).
991203String requester In certain cases the string requester led to unpredictable results. BUG
991201Mtprgn A new flag 'M' has been introduced to allow to take structures from a .mab file.
991201srf/d/s Surface picking nid not work in all cases. BUG
991130mch/t/p Transformation parameters are printed in more detail. The axis of a transformation can be displayed.
991118rosrch
acdsrch
mdcmsrch
Three scripts are available to produce a ranking of the available compounds of either of the three databases rosis, acd, and medchem97 with respect to a given topological pharmacophor (see Topological Pharmacophors).
Start the scripts at the Basel site on a multiprocessor machine, preferably on rbaw01!
991118mch/q The flexible match has been improved by adding a phase of free minimization to release possible strains induced by the constraints.
991111Mtprgn
php/w
The default critical distance for hydrophobic agons has been increased to 10 A.
991110opt/e/n/t Themodynamic quantities for vibrations can be calculated.
991110opt/e/n In addition to deformation modes, vibrational normal modes can now be calculated.
991108Mbcd A new option, -a, has been introduced which causes all agons to be considered of type Anyatom.
991108mch/d/h A file of (rooted) topological pharmacophors can be written, to perform similarity-diversity analyses.
991108Mtprcnt Analysis of size-distribution of topological pharmacophors (see Associated Programs).
991104lib/n Libraries can be defined by reading a file containing a list of names of entries to be included in the library.
991026Home Page A tutorial on molecular surface handling has been written.
991022mch/s Substructure matching can now also be performed by pairwise rigid-body matches in addition to multimatching (switch 2/1).
991021mch/s The fragment recognition routine has been improved.
991007xnr/s NMR ring-shift positionning has been augmented by adding an additional algorithm and several interactive features.
990930xnr/s A molecule with magnetic ring current can be positioned with respect to a structure for which NMR-shift changes have been measured that occur upon binding of the molecule to the structure.
990929Mdltcat The price-quantity filter for compound sets from the ACD-catalog database (in Daylight format) has been extended to enable extraction of the FCD-codes and to provide an estimate of the total price.
990920 When several entries must be specified a library selector apears first (if libraries exist). The entries of specified libraries then already appear as marked in the subsequent entry selector.
990827 Any selection of several entries will first present a list of libraries to specify library-wise. Subsequently, a selector for entries will be presented with the members of the specified libraries already marked.
990826lib/f Libraries can be filtered with respect to several properties of their members. Current filter criteria are: number of heavy atoms, number of N and O atoms, number of H-bond donors, and ring condensation number.
990615pca/p/i/c Distances of neiboring atoms from the central atom can be displayed.
990614mch/q Flexible superposition has been implemented.
990611 Monitor reset after use of window stereo has been modified to make it work on new origin machines.
990610 Dot- and edge-representations of surfaces are modulated by the same alpha value that governs the transparency of their faces.
990608 For sliders and parameter table the cancel button has been replaced by a reset button, which leaves the slider (table) on the screen and just resets the values.
990520lib
.../n,+
A new main menu has been introduced to cover activities with libraries (formerly called entry sets). Most of the current menu options were previously located in .../n. This latter menu has been renamed to .../+, and is now restricted to single entry manipulations.
990520php/a/e Agons can also be specified in the set menu.
990520php/a/r All excluded volume agons of the current pharmacophore can be removed at once.
990520mch/q The superposition with respect to similarity of topological pharmacophore description has been generalised to include pharmacophore-type entries.
990505Mtprgn
Mtprsml
php/w,v
mch/q
.../n/b/q,i
A new batch-facility, Topological Pharmacophores, has been introduced (see corresponding tutorial). Together with it go a couple of options within Moloc:
- to produce topological pharmacophore files from structures or pharmacophore entries
- to superimpose structures according to similarity of their topological pharmacophore description.
- to print out the topological pharmacophore data and to change the parameters that enter these data
990322 The command replay feature has been extended to allow for slider settings as well. (Command replay is only available in Molox!)
990319cnf/m/m
cnf/m/j
Conformation libraries can be moved as a whole with a specified transformation. The old merge option (m) has been changed to j (join).
990311pca/c/o/e/n
dyn/n
Normal mode analysis for C-alpha structures has been implemented. As in the case of all-atom structures the result can be written onto a trajectory file (.mcc) and then be reexamined in menu dyn/n.
990308pca/c/o/c/d Distance constraints did not work properly. BUG
990304 The slider utility has benn modified to enable help on single sliders (with right hand mouse button). Cancelling made changes is also possible. Help texts will be inserted in the future.
990304 A small program 'Movie' has been written which generates a trajectory file .mac from a given initial structure (.mab file) and a transformation (.trf file) leading to the final structure. The number of steps can be specified. View the trajectory in dyn/v.
990303.../g/a CHARMM coordinate files can be read.
990302srf/m The surface move menu has been augmented by the possibility to apply a transformation, by a reset button, and by the calculation of a final over-all transformation.
990212 A www page 'File Formats' has been introduced into Moloc's home page. It contains the format of .sfc and .plt files as well as comments on .pdb files. Further file descriptions will follow.
990212pca/p/i After leaving the isolated-atom scan utility, the individual atom markings and labellings are restored.
990211srf/e The center of the environment can now be defined as the centroid of a set of atoms.
990211.../:/m Ball and stick representation can be achieved in five levels of detailing (zero to four). This detailing level can be either fixed or adjusted automatically to ball and stick diameters as they appear on display. For large structures drawing performance can so be improved. This feature works only in the OpenGL version (Molox).
990211xnr/p Coloring of single atoms or monomers (a) and by atom- or monomer-properties (p) has been implemented.
990205xnr/p This protein display menu contains a new option 'f' which allows to color proteins residue-wise according to a color code red from a sequence type file.
990205xnr/b A new submenu has been introduced which allows to display Bragg scattering planes.
990202opt/e/w/o This new option allows to direct output to a file.
990202.../g/p Space groups of pdb files with full monoclinic nomenclature have sometimes be incorrectly read. BUG
990104.../q/q,r Insertion of comments has been modified to avoid picking. Option r has been added to keep the functionality of deleting comments by picking them.