Moloc Updates |
Recent | 2014 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 |
Moloc Home |
---|
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.