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Updates 1998

Updates 1998


Date   Menu Option  Description of Change

981216 .../f/i      The ikon type on foto-sized displays can be chosen.
981214 .../:/g      Printer options were incorrectly read from startup
                    files. BUG
981214 xry          A tentative utility for protein X-ray model building has
                    been created to combine the most frequently used options
                    in a single menu (crystallographers workshop).
981214 .../g,s      Storing and reading surfaces (including comment entries)
       srf/g,s      has been moved from the srf menu to the general get/store
                    utilities.
981214 srf/d/s      In connection with the comment utility, surface picking
                    has also been enabled for the IRIX-gl executable Moloc.
981214 .../q        A new utility qmt (comments) has been introduced. It
                    allows to add positioned comments which can be stored
                    to and retrieved from disk files. The file type is .sfc,
                    indicating that comment entries are treated as a type
                    of surfaces. Correspondingly, their visibility is also
                    governed in option m.
981211 Mbcd         The directory structure of Catalyst has changed with the
                    new version 4.0. For that reason Mbcd failed. Mbcd has
                    now been adapted to the new directory structure, and will
                    not work on earlier versions of Catalyst any more.
981201 .../p        Surfaces now also appear on PostScript files. However,
                    only vertices and edges are displayed. Faces are omitted.
981116 pca/p/i,p    The forge option has been introduced into the protein
                    scanning menus to allow for immediate action upon
                    detection of awkward structural features.
981116 frg/b        A new option has been introduced to allow to modify
                    B-factors and occupancies of a set of atoms.
981112 .../s        Disc-storing entries carrying a custom-defined color
                    failed. BUG
981106 .../s/p      Writing non-polymer entries worked incorrectly or even
                    led to a crash. This has been fixed. BUG
981106 .../g/p      Moloc crashed when unorthodox space group nomenclature
                    was given (e.g. C2 instead of C 2). It was tried to fix
                    this, though it may not work in all possible cases. There
                    are many possible deviations from the norm!
981029 .../g/p      CONECT records from .pdb files were not properly read. BUG
981029 Home Page    A short tutorial on diversity analysis has been added.
981028 geo/c        Geometry data are cleared as before. However, to clear
                    printed text (option shift a) the shift key must also
                    be pressed.
981027 dyn/v        Entries on the trajectory may be set invisible for
                    examination (though they must be set active upon entering
                    the view menu in case of multiple entry trajectories).
981022 dyn/t/k      A new option has been introduced which can calculate
                    two-dimensional histograms of quantities evaluated
                    along a dynamics trajectory.
981021 dyn/t/e      Values of total energies along a trajectory can be
                    analysed.
981020 dyn/v/d      Switching from disk mode to buffer mode failed. BUG
981019 .../n/b/s    The command mode has been generalized to work in all
                    menus. Correspondingly, there is no more option s in
                    the browse menu. See the tutorial on the Moloc home
                    page for instructions on how to use the command mode.
                    This feature is only available in the X-version Molox.
981013 mch/d/a/w    An auxillary program Mdltcat (located in the same
                    directory as Moloc) is available which filters out
                    supplier information from DAYLIGHT's ACD database for
                    the compounds of the list, written by this menu choice.
981012 .../v        O2 machines are able to operate in widow stereo under
                    IRIX 6.5, if they are set up with 32+32 framebuffer
                    depth. This setup is obtained via the facility xscreen
                    and requires superuser privileges.
981002 php/c        Hypotheses from .chm files (BIOCAD format) can be read
                    into Moloc as pharmacophore entries.
981002 dyn/t/n      Proton NMR shifts due to magnetic shielding of benzene
                    rings can be calculated over a trajectory.
980930 mch/d/a      The output for output levels 1 to 3 has been altered to
                    allow direct input into DAYLIGHT database software.
980929 mch/d/a/b    The list of subclusters presented contains an indication
                    on whether a subcluster contains any of the selected
                    elements (1-9,*) or not (-);
980929 mch/d/a      The output level switch has been modified to indicate
                    the number of central elements apearing in the output.
980924 srf/m        Surfaces can be moved around by hand.
980923 .../e/c      Coloring for surfaces crashed when a surface was read
                    in from disc file. BUG
980922 mch/d/a      A switch has been introduced to determine the level of
                    information printout on subclusters [0, 1, 2].
980917 srf/t        The specification of the density of points on the
                    surface has been changed from dots per atom to dots
                    per square Angstrom, which is not atom radius dependent
                    any more. Some special cases with small radii which
                    caused problems before, work now properly.
980915 set/j        When storing a set of atom in .pdb format the directory
                    records (SEQRES, HET, ...) were taken from the whole
                    structure. Now, residues not present in the set are
                    also not listed in the directory records. TER records
                    are omitted altogether.
980914 mch/l        A new option has been introduced in which a set of
                    topologically identical entries can be compared by a
                    cluster tree analysis, with respect to similarity of
                    conformations.
980907 .../s/k      In certain circumstances Moloc crashed here. BUG
980904 .../n/o      Boolean operations can be performed with entry sets.
                    Union, intersection, and complement are provided.
980904 .../n/t      Entries NOT belonging to specified entry sets can now
                    also be deleted.
980903 .../p        In the X-version 'Molox' the picture sizes of PostScript
                    drawings were calculated incorrectly. BUG
980903 xnr/e        Symmetry related copies can be selected according to
                    the criterion whether their centroid lies within the
                    unit cell.
980902 xnr/c        Unit cells are now represented by full parallelepipeds.
980902 mch/t/p      Angle and direction of rotation for any transformation
                    matrix can be printed.
980831 .../g/o      The io-parameter 'marker' can have an additional value
                    'heterogens'. If 'marker' assumes this value the atom
                    markers for heterogen atoms in polymer entries are set
                    but not for chain atoms. For non-polymer entries this
                    value has the same effect as the value 'nonpolymers'.
980831 .../g/p      Bonds specified by CONECT records are ignored if one of
                    the two atoms to be joined is a metal, in accordance with
                    Moloc topology definitions.
980831              Input list files allow to specify two colors for files
                    containing polymers. The entry gets the first color which
                    is applied to all chains. All heterogens that can be
                    identified carry the second color as partial coloring.
980827 cnf/c/c      Automatic setting of stereo constraints was not working.
                    This function has been reinstated. BUG
980819 srf/d/s      For manipulating surfaces a new option (c) is available
                    which provides the possibility to delete a connected
                    fraction of a surface by picking a single vertex.
980819 srf/d/s      Picking of surface vertices or edges has not worked
                    properly in all cases. BUG
980819 mch/s/l      In substructure matching the specification by SMILES has
                    been generalized to account for cases that would need
                    specification by a SMARTS code.
980817 mch/d        A new option 's' has been introduced which offers the
                    possibility to only examime a subset of the structures
                    by using the corresponding submatrix of the current
                    similarity matrix. (The previous option 's' has been
                    renamed to 'p').
980814 pca/p/p      When scanning through residues using an old calculation
                    of RSCC values, the program crashed, when residues had
                    been deleted in the meantime. This has been mended such
                    as to jump over missing residues. BUG
980814 mch/d/d      In cluster analysis two new options have been introduced.
       mch/d/r      If an analysis of subclusters has been made (options s,
       mch/d/a      l, or c) option b provides the possibility to examine any
                    branch of this analysis by choosing it, while option n
                    allows choose a branch by giving a name of one of its
                    entries.
980812 mch/d/l      The substructure definition by SMILES code has been
                    generalized to handle multiple SMILES codes in order to
                    deal with cases that need specification by a SMARTS code.
                    Compulsory H-counts can also be specified.
980728 .../g/i      Reading C-alpha structures from .cif files resulted in a
                    reversed order of the residues in memory. This caused
                    problems in homology building or protein updating.Now the
                    residues are arranged in conventional order.
980728 pca/u        Updating proteins has been mended to avoid crash for cases
                    with disulfid bridges. BUG
980727 opt/e/w/a    Hydrogen bonding strengths are given for all heteroatoms
                    even if they are not considered H-bonders (halogens).
980722 pca/p/w/g    Geometry display is now cleared upon leaving.
980722 .../e        Labelling of isolated atoms has been introduced here.
980630 srf/d        A new type of "surface" object has been created to
                    display data in three dimensions. If a "surface" is of
                    this type this menu takes a different appearance, suited
                    to manipulate the graph. The hydration summaries
                    produced in srf/h are an example for such objects.
980630 srf/h        Hydration calculations have been updated to conform with
                    the new MAB force field. In addition to writing hydration
                    values to the charge field of the atoms, a graph of the
                    hydration profiles is produced. Optionally, a summary of
                    descriptors for the profiles can be displayed in three
                    dimensions.
980611 srf/d/c      In addition to electrostatic potentials the electric
                    field component normal to the surface can be displayed.
980611 opt          The H-bond pattern calculation has been modified to keep
                    the old pattern whenever the new one has less bonding
                    energy. This avoids difficulties with the minimizer.
                    For dynamics calculations this feature is inactive.
980610 srf/d/c      Two modes of coloring have been added. They display the
                    electrostatic potential due to atomic charges without
                    and with inclusion of hybridization dipoles.
980610 opt          The range of H-bonds has been increased. Interaction
                    extends now to distances 2.5 Angstrom (before 1.0) above
                    the distance of minimal energy. This range has again been
                    modified such that H-bonds reach somewhat less far than
                    the v.d.W. cutoff. For the actual form of the potential
                    see the graphical display which can be generated in menu
                    opt/e/g/h.
980609 srf/a        Atomic charge calculation has been modified. In addition
                    to MAB atomic charges, the hybridization dipole moments
                    can be accounted for by corresponding charge shifts along
                    bonds. In addition, charges on hydrogens can be increased.
980529 dtp/p        The generation of SMILES codes became incorrect
       .../s/l      following switch over to the new MIPS Pro 7.2 compiler.
                    The difficulty manifested itself in various places
                    where this functionality is used. BUG
980526 .../g/d      Reading of GROMOS files has been generalized to keep
                    or omit explicit hydrogens. Heterogen atom recognition
                    has been improved. This eliminates generation of
                    erroneous connectivities of previous versions.
980515 .../:/r      Writing RGB files did not work for some time, now it
                    does again. BUG
980513 srf/d/e      A new menu has been introduced in which surface
                    tessellation can be modified by hand. This is useful
                    in cases where automatic tessellation is unsatisfactory
                    due to irregular surface point distribution or due to
                    the presence of cusps or sharp ridges.
980512 srf/d/c      Surfaces can be colored according to H-bond donor and
                    acceptor strengths as experienced by a hypothetical
                    water molecule positioned on the surface.
980508 .../g/s      Shellx files contain z-values defined differently from
                    usual convention. Moloc now replaces these values by the
                    conventional ones. BUG
980508 srf/d/t      The surface tessellator has been improved.
980506 srf          Surface representation has been fundamentally changed.
                    Consequently this menu contains many modifications and
                    several new submenus. Surfaces can now be rendered in
                    (transparent) solid form, as meshes, or (as previously)
                    in dotted form. Technically, surfaces are now new
                    objects in Moloc in contrast to the earlier (still
                    available) case, where they were a special type of
                    entries. For these new surface objects there is also a
                    new file format (.sfc). For details, see online help in
                    the 'srf' menu and in its submenues.
980505 .../g/d      The new GROMOS96 file format for structures and
       dyn/w        trajectories can be read. Recognition is automatic.
980505 .../g/f      For missing crystal information, available coordinates are
                    now taken as kartesian. (Program used to crash) BUG
980504 xnr/d/r      The modified newer .upl format of DIANA is also read.
980406 .../:/h      A new switch "key control" (inactive by default) has been
                    added. If active, the program can be operated by key
                    strokes (except for picking operations). In the setup
                    file this switch carries the label "keycntl" and can have
                    the values "yes" or "no". Only available in Molox!
980403 .../g/i      When reading Calf structures from .cif files, the
                    arrangement of residues in memory was reversed from the
                    sequence appearing in the file. This led to problems in
                    case of chain breaks. This has now been changed. BUG
980331 .../g/p,q    Monoclinic space groups are also recognized from their
                    extended Herrmann-Maughin symbols.
980330 dyn/n        Normal modes, stored as a .mac file, can be read back from
                    disc and be redisplayed as vectors or as animation.
980330 opt/e/n/w    The result of a normal mode calculation can be stored as
                    a .mac file (trajectory format).
980330 opt/e/n/f,a  Normal modes can be examined one by one by showing an
                    animation of the corresponding deformations.
980326 map/g        Reading of compressed mask maps, produced by the MAMA
                    software, has been amended. BUG
980326 .../g/k/w    Multiconfomation files from the software package DIANA can
                    be read in as conformation libraries in Moloc.
980325 .../s/s      When writing .shx files the ZERR record is also taken from
                    the input file, if available.
980323 Msrfvl       Total number of donor hydrogens and acceptor lone pairs
                    from N- and O-heavy atoms are also evaluated.
980313 opt          MAB force constants for dihedral terms of bonds with
                    double bond character and for pyramidality terms of
                    sp2 centers have been doubled!
980313 .../e/b      For Calf structures, when setting radii for balls and
                    sticks, a PIPE or RIBBON representation can be chosen
                    (see help). This feature is restricted to the Molox
                    (OpenGL X) version.
980311 xnr/i        The fine checking of environment distances may take much
                    time. Thus, the user is now asked whether he wants this
                    checking done.
980311 pca/o        A new menu has been added for the organization of data
                    relating to polymer properties. It allows to add (remove)
                    such information to an entry, to arrange sequence streches,
                    to find orphan atoms and assign them to monomers, and
                    to unite monomers. Additional functionality may be added
                    according to needs.
980309              With the introduction of the new ORIGIN server all
                    programs will be newly recompiled. The resulting binaries
                    will not run on the old IRIX 5 operating system.
980309 geo/w/g      Rms-distance values have actually been ms-values. This
                    has now been corrected. Similarly, the values d0, d1,
                    and d2 in the output of the batch program Msrfvl have
                    been changed from ms-deviation values to rms-deviation
                    values.
980305              The auxillary program Gr2d which displays 2-dimensional
                    graphs, has been ported to OpenGL-X. This makes it usable
                    on OpenGL-capable X-window terminals (e.g. on PC's with
                    ReflectionX).
980205 .../p        Writing PostScript files needed modification because of
                    change in zooming mechanism.
980204 .../n/u      A selection of entries can be united into a single one.
980204 .../e/b      Ball and stick drawing has been improved in Molox.
980204              The zooming had to be changed because of technical reasons
                    with the new graphics library OpenGL. Both binaries, Moloc
                    and Molox were changed for consistency reasons. This change
                    entailed several additional alterations, and some may be
                    needed in the future. So, be patient!
980130              Redering speed of ball and stick models has been improved.
980129 .../:/*      Handling of lighting conditions has been reorganized.
                    Lighting in OpenGL has been mended (is still slow!).
980114 .../e/z      The monomer information of a polymer can be removed. The
                    corresponding entry is than considered a non-polymer. This
                    is usefull when using parts of a polymer as starting point
                    for modelling new inhibitors.
980114 opt          The treatment of sulfates and analogous hypervalent 2nd
                    row element systems has been amended. BUG
980112 .../s/m      .mab files now can hold polymer information in order to
       .../g/m      speed up the preparatory phase of the force field
                    calculation in batch mode. These files are the input for
                    starting a batch calculation with the program Mabch.
980112 opt          In various places the force field may be called as a tool.
                    The setup menus now keep once set values as defaults for
                    the next call at the same place. The different places keep
                    individual defaults.