Moloc Updates |
Recent | 2014 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 |
Moloc Home |
---|
Date | Menu-Option | Description of Change |
---|---|---|
050203 | .../g/s | Reading SHELLX files has been updated to account for new formatting of SFAC records. |
041117 | MAB | The force-field parameters for pi-systems habe been modified slightly to better account for pyramidality at hypervalent nitrogen atoms. |
041003 | .../e | This menu has been rearranged: option 'i' has been moved more to the beginning, where markers and labels are handled. |
041003 | Mol3d | A new option, 'c' has been added by which data fields of partial atomic charges can be added to the result file. The previous option 'c' (center and principle axes orientation) has been renamed to 'z'. |
041002 | mch/q | The descriptor file for matched pharmacophores can now (optionally) also contain the similarity value of the match, together with the identification of the atoms that are paired up. Furthermore, the result for several poses per molecule can be written to the file. |
040929 | dTp/c | In some cases of unadvertent picking strange atom types could be produced. This has been mended. BUG. |
040927 | mch/c | The option has been upgraded to also perform structure superposions for fixed-atoms and fixed-axes cases. |
040922 | lib/q | Scoring of a set of ligands with respect to a receptor can be calculated via a modified Boehm algorithm. This is a generalization to several ligands of option Srf/b. |
040921 | dTp/m Msmab | Recognition of SMILES codes has been improved. Some cases of cis-trans stereo flags could not be interpreted previously. |
040921 | lib/f Mfltr | An additional filtering criterion, largest unbridged ring, has been added. |
040920 | xry/p pca/p/p | A new option, 'r' (real space refinement) has been added, to enter directly the real space refinement menu with the atoms of the residue under examination as a predefined set. Option 'o' allows to specify automatic inclusion of a neighborhood. |
040916 | xry/s/o pca/c/s/o | During the examination of the results of a loop search for proteins, the searched part of the C-alfa structure can optionally also be displayed in all-atom representation. |
040915 | xry/e | A copy of the main menu item 'Map' has been installed in 'xry' under the letter 'e' (electron density maps). |
040915 | map,php,srf dyn,xnr | In the main menu the items map, php, srf, dyn and xnr have been renamed to Map, Php, Srf, Dyn and nxr, respectively. This, to enable unambiguous menu choices with the keyboard in the key-control mode. |
040909 | mch/p | The menu for pharmacophore matching has been reorganized and extended. It is now possible to define fixed atoms and axes in order to perform a restricted match. |
040907 | mch/p | Specification of target and moved structure for pharmacophore matching is now done via a selector. Previously they needed to be picked. |
040903 | mch/d | The menu for diversity analysis has been reorganized. All options to identify special atoms for restricted matching conditions (fixed atom, axial) have been delegated to a submenu which is reached with option 'i'. |
040901 | frg/s,n | Forging pharmacophore entries did not work properly. This has been mended. |
040820 | .../k/m | Writing of unformatted files has been made platform independent. This affects only the storage of Moloc conformation libraries (.mcl), the only unformatted file type written by Moloc. |
040819 | map/g | The reader for unformatted files has been updated to account for platform dependence. |
040818 | Mol3d Msmab | The generation of conformations of condensed rings in the ab-initio coordinate generator has been modified to improve on 6-rings. |
040818 | .../:/i | TIFF image files for Linux are now written in uncompressed mode (COMPRESSION_NONE) because many image processing programs are unable to read COMPRESSION_JPEG. This leads to increased file sizes (at least 1 order of magnitude). |
040813 | Guided Tour | A new tutorial on Template Matching is provided. It describes the activities of 'Soft Subset Minimizations' (opt/SHIFT's') and steps needed in 'Template matching' (lib/m) for a simple example. |
040812 | mch/d | 3-d pharmacophore similarity calculations for structures in given (unchanged) orientations can now directly be performed by specifying as superposition mode 'o' (omit match). This may e.g. be helpful for the analysis of the results of docking calculations. |
040805 | .../:/i | Writing a bitmap image file has now also been implemented for Linux. The file format is TIFF (extension .tif), using a jpeg-type compression algorithm (COMPRESSION_JPEG). |
040723 | lib/m | With this new option the user can match each member of a set of templates onto a set of geometrical conditions, consisting of positions and corresponding exit vectors. A ranked list of matched templates is returned. |
040723 | lib/m,f Mfltr | The menu item 'm' (define library of multi-fragment entries) has been moved to the general filter utility 'f', where one can now specify the maximum number of fragments a structure may contain. The corresponding option is also available in the batch program Mfltr through the parameter '-f'. |
040723 | opt | The setup menu for MAB force-field calculations has been reorganized. Some more seldom-used options have been moved to shifted options, i.e. they can be accessed by clicking an option with the SHIFT key pressed. Among those are: SHIFT 'w' (previously 'v'), resets the weights; SHIFT 'r' (previously 'p'), distance positioning; and, newly, SHIFT 's', define a 'soft set'. |
040723 | opt/s | When chosen with the shift key pressed (SHIFT 's'), this new option allows to define a set of atoms ('soft set'), among which the MAB force-field constants are reduced by a user-specified factor. One possible aplication is to find out by energy minimization, whether a 'template' exerts forces on its substituents, when they bind to a receptor. |
040723 | .../e/b | For pharmacophore entries, setting a non-zero atom radius yields now a cone representation for directed agons. |
040721 | Mfltr | A new option, '-y', has been introduced which allows to filter files written in .mol2 format instead of the default .sd (.mol) format. |
040721 | Mfltr | The parameter for ring condensation could not be modified, because its letter, 'r', coincided with option 'redirect'. Thus, the letter 'k' now governs ring condensation. BUG. |
040719 | .../:/h | A new switch, "libselect", has been added, which causes the selection of several entries to be preceeded by a selector for libraries and visible entries. By default this switch is set. Library preselection was always active before adding this switch, i.e. this feature is now optional. |
040716 | lib/o | A new logical library combination, "exclusiv", has benn added. The selector for a logical combination has been equiped with help text. |
040709 | Mclsn | This new batch program reads a similarity file (.sml) and performs partitional clustering(s) on the bases of shared neighbors. |
040702 | Msrfvl | Option 't' has been modified and extended. It now requires a number which governs the type of returned information. Atom hybridization, donor- and acceptor strengths are given if bit0(1), bit1(2), bit2(4) are set respectively. Thus, for a value of 7 all three quantities are given as before. In addition, setting bit3(8) causes output of a list of H-bonds. |
040628 | frg/j | When deleting alternate conformations, atom occupation number were not reset. This has been added now. |
040625 | php/d | In the calculation of the geometrical diversity halogen atoms can now also be considered as potentially polar (H-bond acceptors). |
040625 | php/d | The calculation of the geometrical diversity of polar atoms in a structure has been modified such that the corresponding value for the apolar atoms can also be calculated. Alternatively a product of the two can be obtained. |
040624 | pca/c/h | In certain cases Calf structures of homology models were wrongly connected. This has been mended. BUG. |
040609 | php/j | Residue grained pharmacophores can be generated from Calf structures. |
040605 | menu clan/t | This new toggle option allows to display the labels of the tree leaves alone. |
040605 | pca/s | The sequence analysis menu has been totally reorganized and extended in functionality. |
040602 | .../:/m | An new slider has been added which allows to increase the size of the atom markers. For a non-zero value markers are drawn as polyeders and hence vary in size with zooming. The value can be stored in and reloaded from the startup file under the label 'atomsize'. |
040525 | pca/r/p,e xry/r/p,e | Real space refinement parameters can now be saved to file (in option .../:/s) and be recovered in later sessions. In the startup file, .Moloc, they appear in section ">ForceField" and start with RSR. |
040525 | frg | Combinations of various forge activities led in unfortunate circumstances to a program crash. A corresponding correction has been implemented. BUG. |
040522 | dyn/g/r | For structures without explicit hydrogens the .cif file for REFMAC did not contain bonds. This has been corrected. BUG. |
040522 | entry selector | When selecting entries the new preselection button "all visible entries" has been added. |
040521 | xnr/u/s,o | The new option 's' allows to examine subtrees of a ring superposition tree. The subset is specified by a list of leave names, read from a file. The previous option 's' (superposition) has been renamed to 'o' (overlay). |
040517 | menu clan/o | A list of entries in tree-leave order can also be written onto a file, not just to the text port. |
040517 | menu clan/w | Visible entries can also be written to .cif files (with or without tree). |
040517 | xnr/u/k,q | These options replace the previous option 't' to calculate and examine ring-diversity trees. Newly, trees are not destroyed upon leaving examination, and can be reexamined (option 'q'). Additionally, diversity matrices can be written to file, and then be reexamined, again with option 'q', in a new session, provided the corresponding rings have been previously reassigned. |
040517 | xnr/u/c | This new option allows to set (change) the color of rings. |
040505 | frg/h | A reset option (Ctrl-key + Shift-key + middle-mouse-button click) has been added to the chi-angle modification of protein side chains. |
040504 | lib/c | Interactive docking has been extended to also include an electron density map as target object. |
040427 | xnr/u/r | Automatic ring search has been added. |
040426 | php/d | This new option calculates polar geometrical diversity (mosaicness) of a set of structures. Its value depends on a user-given scale. |
040421 | map/g | The default extension of CCP4 maps has been changed from .ccp to .map. |
040415 | dTp/p lib/d/r | SMILES codes do not include hydrogen atoms even if the molecules contain explicit hydrogens. |
040330 | srf/b | The free-energy scoring function has been reparametrized to conform with the new force-field parametrization. |
040303 | .../g/p | Alternate location reading failed when not all the records of an atom followed each other immediately. This has been mended to the extent that alternate location records may occur anywhere within the span of the corresponding residue. |
040219 | lib/c Mdck | A H-bond pattern calculation has been added to the pharmacophore-docking algorithm. This restricts the number of H-bond donations (-acceptions) of any atom or agon to the respectively specified maximum numbers. |
040212 | Mtree | New flags, -a, -t, have been added to perform a similarity analysis with optional similarity descriptor generation. Also a verbose flag, -v, has been added. |
040211 | Mtree | A new flag, -d, has been added which causes the program to write additional columns with dissimilarity (distance) values from the branch centers. |
040211 | .../g/a Mamber | Amber-type file reading has been updated to also cope with the new topology-file format. |
040205 | set | When entering the set menu and no free set is available, the user is now requested to free at least one set. |
040128 | xnr/e,i xry/y/e,i | Atom-coalescence checking has been introduced as a choosable option. If omitted, calculation time of symmetry copies can be substantially reduced for large structures at the cost of possibly having coalescent atoms. |
040122 | pca/t/r | The protein-threading menu has been extended by option 'r' which allows to completely replace the sequence of amino acid residues on the test structure. |
040116 | Moloc | A menu-path search utility has been implemented which yields all menu-path's in Moloc, for which the menu item or help-text contains the keywords provided by the user. For instructions about usage consult help to 'exi' (select 'exi' with the Ctrl-key pressed). |
040116 | Mtree | This new batch program reads a similarity matrix in Moloc format and performs a hierarchical clustering. The result may be written out in Newick format or as a table giving in columns the subcluster identifiers, which result from clustering at specified similarity levels. |
040108 | pca/t | This new menu provides the possibility to thread protein sequences onto a Calf structure. Energy evaluations are performed within the Calf force-field of Moloc. |
040108 | .../:/d | Dashed lines can also be directed (decreasing dash lengths). |