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Updates 1997

Updates 1997


Date   Menu Option  Description of Change

971218 .../s/i      The cif file can now contain atomic charges. They are
       .../g/i      automatically stored onto file, and read when available.
971217 cnf/c/b      Background entries are now stored as .b.cif files in order
                    to retain any possible polymer information (to speed up
                    the preparatory phase of the force field calculation).
971217 pca/c/s      Peptide vectors and C-beta are correctly displayed when
                    viewing the results of a fragment search. BUG
9712xx              The manual for Moloc has been updated. The chapters after
                    the introductory one are just repeating the online help
                    texts. Consequently, most online help have been completed
                    and been brought up to date.
971127 mch/s        Fragment recognition improved. BUG
971110              Picking in Molox has been amended. BUG
9711xx opt/e/n      Normal modes of deformation (not vibration) can be
                    calculated and displayed.
9711xx              Online help has been augmented by a search option, which
                    is activated by selecting the question mark with the
                    control key pressed. Search covers just the current
                    menu.
971015 opt/e/a      Atomic hybridization dipoles are printed when atomic
                    charges are calculated.
971015 srf/a        The calculation of atomic point charges has been
                    standardized to utilize the new force field with a special
                    parameter set to account for the omission of atomic
                    hybridization dipoles.
971014 geo/w/m      The electric dipole moment of a molecule with given atomic
                    point charges can be calculated.
971014 geo/w/a      A threshold can be set for the interpretation of geometry
                    data of sets (see geo/w/g).
971014 geo/w/g      The comparison of geometry data of two sets of atoms has
                    been generalized to deal with one- and two-atom sets as
                    well.
971013 mch/s        Fragment recognition improved. BUG
971013 pca/p/i      List of calculated data fixed. BUG
971007 .../g/p      The Naming of the N eta atoms of arginin has been changed
                    to conform with the UPAC rules.
970926 opt          The valence angle bending potential has been modifies for
                    the case of large angle values, to yield a somewhat higher
                    barrier.
970926 dTp/k        Adding explicit hydrogens may optionally exclude aliphatic
                    carbon atoms.
970923 .../s/m      Writing and reading of .mab files now includes atomic
                    charge values.
970923 opt/m        The case of working with input charges has been put on a
                    somewhat more systematic footing.
970923 mch/s        Substructures of a set of entries can be matched on top
                    of each other. Recognition of the (connected) substructures
                    is automatic. The multimatch algorithm is used.
970922 mch/m/h      For pairwise matching of two Calf strustures, pairs of
                    corresponding Calfs can be specified by reading a file of
                    the format used in homology building.
970922 opt/c/l      List for positional constraints shows upper and lower flag.
970918 pca/p/p      The scaling factor for the RSCC calculation has been
       pca/p/i      modified.
970918 xnr/j        Chosen color is now accepted. BUG
970917 pca/p/p/t    The sliders for setting the thresholds now also show the
       pca/p/i/t    average and rmsd values for user information.
970917 pca/p/p/g    Access to the geometry tool has been inserted in the menu.
970917 srf/c        The surface coloring option has been moved to the entry
                    display option .../e/c and H-bond and charge information
                    are kept on the .jkl surface files.
970916 .../g/k/p    Multiconformer structures on .pdb files can be read as a
                    Moloc conformation library. This is usefull for solution NMR
                    structures in which the conformations are indicated by the
                    keyword MODEL.
970913 pca/p/p/p    In the residue scan menu a list of the actual values of
                    the calculated quantities can be printed.
970821 geo/a        Text of up to 127 characters can be attached to an atom
                    position.
970808 opt          The half width angle of H-bond donor has been modified to
                    46 degrees. Acceptors have 60 degrees.
970808 php/g        Hypotheses out of Catalyst can be read into a Moloc
                    pharmacophor via a file of .filtlog format.
9708xx              The graphics part of Moloc has been rewritten using the
                    more modern OpenGL graphics language and the X-windowing
                    system. Thus, at present two executable files exist:
                    Moloc, which performs best on older SGI machines, and
                    Molox for the newer machines. Molox can also be used
                    from PC's over the network when a OpenGL-capable
                    X-emulation, such as ReflexionX is available.
                    This is a major modification and we expect to have to
                    deal with straightening out activities for some time.
9706xx opt          The H-bond strengths in the force field MAB have been
                    improved by applying a modified preparatory calculation
                    (JCAMD in press). This is a major change and uncovering
                    of bugs and other modifications are expected to go on for
                    some time to come. The old force field can still be used,
                    in particular in cases where obvious errors show up.
                    In the course of this modification new features are
                    available, such as the examination of pi-orbitals (opt/e/o)
                    ore the examination of donor and acceptor strengths of
                    polar atoms (opt/e/w/a).
97xxxx dyn/g/g      GROMOS topology files can be written in the new GROMOS96
                    format.
97xxxx pca/p/i,p    Scan options for residues (p) and isolated atoms (i) have
                    been unified and based on the same calculation. The
                    quantities of interest are only calculated once unless
                    the user specifies otherwise.
97xxxx pca          Geometry (g) and forge (f) options have been introduced
                    here to facilitate repeated use of options m, r, and p.
97xxxx pca/u        Full (all atom) proteins can be updated from a C-alpha
                    structure also in case this has been augmented in the
                    Calf builder. For the exact procedure consult the online
                    help.
97xxxx              When starting Moloc with a file name on the command line,
                    file reading can be governed interactively by adding the
                    flag -i (see by starting Moloc -h). This can be usefull
                    when starting Moloc automatically for e.g. a .pdb file
                    as may be the case in WWW applications.
97xxxx mch/t/f      In addition to the old Moloc .trf format, transformations
                    can be written and read in 'O' format (file type .tro).
                    This latter is the default.
97xxxx dyn/g/t      Writing of TNT geometry files has been modified (removing
                    kommas) to obey TNT-convention.
97xxxx mch/d/r      A previously performed similarity calculation stored on
                    a .sml file can be reexamined by reading the file. The
                    corresponding entries must be read in beforhand (e.g. from
                    a .mab file stored under mch/d/f) and are then assigned
                    automatically.
97xxxx mch/d/d/g    A previously stored selection (.smi file) can be retrieved
       mch/d/r/g    for repeated examination. No additional structures are
       mch/d/a/g    entered into Moloc, but the old marks for selected entries
                    are replaced by the new ones indicated on the file.
97xxxx dyn/y        Polar hydrogens can be added ito conform with the hydrogen-
                    bonding pattern as calculated by the MAB force field. This
                    includes the conformation of hydrogens which are not
                    engaged in a bond themselves, but have restrictions because
                    a lone pair accepts a hydrogen bond.
97xxxx srf/e        Option is also effective for Connolly surfaces.
97xxxx frg/k        Coordinate transfer from one entry to another can also be
                    specified residue- and entry-wise.
97xxxx set/j        In addition to .jkl files a set can be sored as a .pdb file.
97xxxx mch/r        Several entries can be specified to be relocated at once.
97xxxx frg/h,l      Picking the auxillary peptide display (pepdide planes, side
                    chains) is disabled. BUG
97xxxx xnr/j        Immediately updated equivalent cristallographic positions
                    also show atom markers and -labels.
97xxxx pca/c/s/d/+  The results of the loop search can be viewed by cycling
                    forwards and backwards through the hit list.
97xxxx pca/c/s/d,e  Actual sequences of segments found in the database are
       pca/m/s/d,e  given in screen help
97xxxx frg/l        Actual phi-psi values are indicated in menu header when
                    turning peptide links.