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Date | Menu-Option | Description of Change |
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141214 | startup | The label-font and it's size can be specified in the startup file, .Moloc (Linux). |
141013 | cnf/m/q | This new option allows to arrange the conformations in a library according to increasing values of a selected quantity, such as e.g. energy. |
141013 | cnf/m/o | This new option allows to perform a energy minimization on each conformation. This is a free optimization which does not allow for fixed atoms, constraints or a background entry! |
141011 | cnf/c/b | Conformations analysis with a background did not work properly. This has been mended. BUG |
141003 | cnf/m/o | Conformations of a library can be energy minimized (e.g. after a topology change). |
140722 | xnr/O | Occupation factors can be displayed, analogously to xnr/t. |
140722 | xnr/e | Alternate locations of symmetry equivalents were not propery transformed. This has been mended. BUG |
140722 | frg/j | Reading and managing of alternate locations (AL) has been modified. Reading now also handles the case when AL's do not immediately follow the atom record, but stay within the block of a single residue or heterogen. |
140707 | .../:/v | With this new option an inverse-video representation can be generated, which should facilitate output for printing. Twofold selection returns to the original display. |
140707 | .../L | This new menu allows to handle the list of entries: option 's' allows to drag single entries; with option 'j' a set of entries can be joined in a contiguous grop; option 'a' enables alphabetic ordering. |
140703 | dTp/s | The substituent adding utility has been augmented by an option, 's', which allows to add fragments in spiro-connection. The previous option 's' (substituent selection) has been renamed to 'f' (fragment). |
140702 | dTp/a | The list of directly choosable atom types has been somewhat enlarged. |
140702 | dTp/s | Two fragments (cyclobutyl, cyclopropyl) have been added to the standard choice. |
140702 | dTp/u | When deleting Hydrogen atoms, the new option has been added to keep the ones attached to polar atoms. |
140702 | .../o, .../s | The line dot-size setting could not be stored in the startup file, .Moloc. This has been added. |
140604 | cnf/c/i,b | The symmetry ambiguity (see cnf/m/s) is already removed in the process of generating conformation libraries. |
140530 | cnf/m/s | Conformations are typically related to the original structure by an operation of the group of topological symmetries of the molecule. This option allows to remove this ambiguity. |
140530 | cnf/n/o | Options for the examination of NOE-violations can be set. At present one can choose between two methods for calculating violations: 1. Any deviation of a distance in a conformation from the value determined by the NOE-measurement is a violation. 2. Only distances larger than idicated by NOE are considered violations. |
140522 | cnf/n/h | This new option allows to modify a conformation interactively by varying dihedral angles, in order to attempt to reduce NOE-violations. This may be helpful in cases where NOE's are from a bound conformation which may differ from any conformation generated in vacuo. |
140517 | cnf/n | The NOE-examination facility has been overhauled and equipped with additional help texts. It allows to find conformations with minimal NOE violations. |
140220 | Mol3d | Mol3d runs a protocol with varying weights for the force-field terms. In the final calculation the weights assume their standard values. For post-minimization with a receptor this type of protocol may lead to results which differ from a straight minimization. As of now, no modification of weights is performed any more in this mode of operation in order to avoid such differences. |
130901 | .../g/b | This hardly used option (direct generation of Calf structure) has been replaced by the possibility to directly read in mmcif files of the Protein Data Bank, without first generating an intermediate .pdb file via 'Mdfy -p'. |
130811 | Mdfy | An option -p has been added which allows to convert mmcif files (For those Moloc's standard extension is '.cim'.) into 'minimal' .pdb files. These have a few non-standard formats (see help, produced by 'Mdfy ?') but can be read as normal .pdb files by Moloc. |
130729 | Dyn/h | The torsional driver tool has been augmented to handle and examine cases of closed rings. |
130620 | Moloc | Picking did not work for very large structures. This has been mended. BUG |
130322 | mch/j/a/m | An additional alignment file format (.msf) can be read. Files of this type are produced by the sequence-alignment editor program xsae. |
130322 | mch/j/a | This new option allows to read alignment files for matching specifications of proteins. |
130322 | mch/j | The multi-match of protein structures has been generalized to also deal with cases having varying deletions and non-identical sequences. In these cases specification has to be made by an alignment file. Transformations of the moved proteins are returned. |
130306 | Linux | Access to 64-bit inode file systems has been implemented in the Linux version. |
120122 | document | A description of the 3d-similarity algorithm has been written. It can be accessed from Moloc's home page (moloc/www/home.html in the download) by going to the Diversity tutorial. |
111126 | nxr/e | Not all space groups are fully treated by Moloc. Several groups (including P-1) have been added to the set of correctly handled groups. |
111117 | opt/e/r | The display of van der Waals distances between polar and apolar atoms did not have an appropriate legend. Now a correct legend is produced. Also the help text of this menu point has been rewritten. |
110713 | Beginner's Corner | A new tutorial has been written which deals with Moloc entry-types and with caveats when modifying ligands that originate from .pdb files. |
110713 | Mtprgn | A new option has been introduced in the generation of topological pharmacophores. It allows to lump together hydrophobic agons, the atom sets of which have immediate neibors. The resulting 'giant agons' eliminate artifacts that originate in differing partitioning of large hydrophobic areas. |
110709 | .../g/l | When reading .tdt files, name tags have been ignored. This has been changed. If a name tag is specified (.../g/o) entries are named by the name specified on the record with the given tag. |
110211 | Moloc | When reading maps specified in an input list file (.ils) the added contouring specification was not executed. This has been fixed. BUG |
100723 | Msmab Mtprgn | A new option -N has been introduced which has to be followed by a string. This string defines the keyword in the .tdt file from which the name of the structures should be taken. Per default the SMILES code is taken as name. |
100603 | Mdfy | This new batch program allows to perform simple modifications of structures. At present, just enantiomers can be generated. |
100521 | Mol3d | Option -E6 produces a list of intermolecular H-bonds and van der Waals contacts. However, there are also repulsive 'H-bond' terms between pairs of exclusive donors or exclusive acceptors. The sum of those terms is included in the vdW-table. Now option -E2 (-E6) also produces a detailed list of the corresponding intermolecular contributions. |
100521 | Mol3d | Addition of hydrogens (option -h) led in certain cases to incorrect stereochemistry. This has been mended. BUG |
100306 | opt/e/i | Option 'd' (write a PostScript file) has been replaced by 'i' (write a RGB-image file). The old functionality is still available if the option is chosen with the SHIFT key pressed. |
100304 | Expert corner | Tutorials on 'Template Matching' and 'Ab Ovo Building' have been updated and augmented by a new one on 'Fragment Libraries'. |
100302 | lib/m/l/i Dyn/o/l/i | Interactive library building has been augmented by a change option. This allows to change singly connected atoms of a structure directly into extensions. |
100218 | lib/t/m,P | During conformation analysis of templates, extensions representing a hydrogen atom may be temporarily replaced by a methyl group to avoid close-contact situations. The same option is available when minimizing fragments in the prune utility. |
100217 | lib/m/l/i Dyn/o/l/i | Interactive library building has been augmented by a forge option. |
100212 | .../s/pdb | pdb-files can be written in pdb-standard version 3. This is governed by the parameter 'pdb-version' in the startup file '.Moloc'. The default is still version 2. File reading handles both versions. |
100212 | pdb | Inosine base reading and writing has been implemented. |
100128 | MAB | The bond radius of fluorine has been increased to a value of .604. The old value of .57 gave rather short bond-lengths to carbon. |
091229 | Mol3d | Option '-E' has been modified. It now requires an integer value. This allows to differentiate the energy output to also allow for lists of intermolecular H-bonds and vdW contacts. |
091118 | opt/a | A new parameter 'Iworry' has been introduced which causes the optimization routine to perform a randomization of the coordinates of the free atoms at each initial start of the force field. This is meant to avoid situations in which the minimizer gets stack in a metastable energy state (e.g. planar). The value can also be specified in the startup file .Moloc in the section 'ForceField'. |
091115 | pca/l | Generates all-atom structures of the peptides given as sequences on a list file. |
091114 | Mol3d | When option -w6 was set, the flag -E had no effect. This has been mended. BUG |
091106 | .../g,s | When writing files, the option 'compress' has been removed. However, file reading still works with compressed files (additional extension '.Z') and now also includes gzip-compressed ones (additional extension '.gz'). This holds not for Windows, where the corresponding shell commands seem to be missing. |
091025 | srf/d/t | Surface tessellation has been improved. For Lee-Richard- and vdW type surfaces tessellation should be made before the surface is stored to file. |
091005 | srf/q | Generation of Connolly-type surfaces has been improved. |
090920 | lib/e/d | Data reading has been extended to also include .tdt files. |
090916 | .../:/*,z | Lighting parameters read from the startup file have not been automatically activated. This has been corrected. BUG |
090913 | .../:/f,z | Fonts can be specified in option 'f' as well as in the startup file .Moloc (X windowing). The option to change font sizes has been renamed from 'f' to 'z'. |
090904 | geo/s | The absolute chirality (CIP) determination failed in complicated situations. A new algorithm has now been implemented. BUG |
090814 | .../g | In rare situations reading several files caused a crash. This has been mended. BUG |
090724 | Msmab | A new option, -w, allows to control the output of data fields for energy and atomic charges to .sd files. |
090724 | Mol3d | A new option, -E, causes the program to write a data field 'MAB_ENERGIES', giving the values of MAB's various energy terms. |
090707 | opt/e/h | By choosing this option with the SHIFT key pressed one can now examine repulsive energy contributions of the MAB force-field between pairs of exclusive H-bond donors or pairs of exclusive H-bond acceptors. |
090703 | pca/m | A new utility has been implemented which allows for mutation of residues in proteins or at protein interfaces. Tools allow to browse through amino acids and rotamers and to evaluate and minimize energies. Surfaces can be displayed for interactive visual examination. |
090604 | MCA | In the C-alpha force field, MCA, the 'valence angle' restoring force has been increased. This avoids instabilities which occurred in certain situations. |
090517 | .../+/f | This new option allows to split up an entry into separate entries, one for each disconnected fragment. |
090514 | Mcnf lib/t/m | Specification of conformation constraints has been changed: yes-no options '-t' and '-c' have been lumped together in a numerical parameter '-c'. A value c=4 causes the program Mcnf to apply the constraints given the input file. |
090513 | Msmab | A new option '-c' has been added. It causes the program to also list conformational constraints in the output file. |
090426 | expert corner | The html page on Calf building has been augmented by a section dealing with the particulars of handling non-natural amino-acid residues. |
090426 | pca/h | This new menu allows to read in non-natural amino acids. They are used when building up peptides containing such residues. A host of utilities (mostly in 'pca' and Calf-building) have been generalized to also handle these residues. |
090326 | Msmab | Enforcement of stereo specifications from SMILES was based on an early, incomplete Daylight manual and could give false results in structures with cycles. This has been corrected. BUG |
090325 | Mol3d | Enforcement of stereo specifications did not work properly. This has been mended. BUG |