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Date | Menu-Option | Description of Change |
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021219 | srf/d/c | Help texts have been added to the various coloring options, which also give explicit values for the applied scales. |
021111 | mch/s | The library produced now consists of the structures containing the fragment instead of the complement set as before. |
021107 | Mfebd | The output has been reformatted. |
021107 | Mol3d | When minimizing molecules together with a environment entry, an additional file is written which contains energy information for each complex. |
021028 | mch/c | Additional clustering methods have been introduced as well as the calculation of the cophenetic correlation coefficient. |
021018 | geo/s | An error that led to a dependence of the result of atomic chirality determimation on the order of bond specification has been mended. BUG |
021011 | mch/c/q | Hierarchical trees can now be stored on file in Newick format. |
021011 | Mfebd | A new switch '-m' which requires a filename has been added. When set, the program only performs a minimization of the provided ligands with the initial receptor and writes the resulting coorinates (including the the ones of the actual receptor) on a .cif file with the specified name. |
020903 | .../g/i | ConQuest-written files (Cambridge Structural Data) in cif-format can now be read. |
020903 | .../g,s/i | Pharmacophore type entries can now be stored to and read from cif-format files. |
020903 | opt/e/e | Entry-wise energy evaluation has been reorganized and made more flexible with respect to choice of options. |
020903 | Mabch | A new switch 'e' has been introduced by which entry-wise energy evaluation can be generated before and after energy minimization. The result appears on standard output. |
020827 | frg/p | Peptide secondary structures were not always built correctly. BUG |
020827 | pca/c/m | When building a peptide for a given sequence, its conformation can be of any repetitive form (before only alpha-helical). The phi-psi angles are taken from the default values, set in option 'a'. |
020823 | selector | In cases where several entries can be selected, ranges of entries can obtain the choice-value of the last selection by pressing the SHIFT key during the next selection. This is a generalization of the common range-choice functionality in file selectors. |
020823 | selector | For multiple choice selections, pressing the ALT key takes over the last choice-value to the next selection. |
020822 | .../e/p | Partial coloring now can also be made to affect bonds with only a single atom in the specifying set. |
020729 | lib/b/s | When browsing through a library (specified with the choice lib/b), this new option allows to make several members of the library simultaneously visible. The visibility selector only presents members of the specified library(ies). |
020705 | dTp/k | The specification of the atoms that should be equipped with explicit hydrogens can now be made more detailed with respect to the hybridization state of carbon. |
020628 | Msrfvl | A new flag '-f' has been introduced. It requires a number which is interpreted as a factor that multiplies the van der Waals radii of all atoms. Its default value is one, of course. |
020628 | xnr/e | Sloppy symmetry definitions in .shx files (e.g. CSD output) are correctly interpreted. Example: 'SYMM -x, .5y, -z' is interpreted as 'SYMM -X, .5+Y, -Z'. |
020628 | srf/d/p/d | Surface vertices can be remove according to distance- an directional criteria with respect to the atoms of a user-defined set. |
020625 | srf/r | For surfaces an additional radius parameter can be set for united atoms. If set to a value larger than the default value of zero, the radius of each atom is increased by this value times the number of the atoms implicit (silent) hydrogens. |
020625 | Msrfvl | The somewhat missleading parameter '-u' (united atoms) has been modified. Now this parameter requires a number, which specifies the van der Waals radius increase, per silent hydrogen, for heavy atoms. |
020610 | set/d,b | The two options 'b' and 'd' have been combined into a single one: 'd' (derived set) The differentiation is now made with an additional selector which also includes the 'entire monomer' option. |
020606 | .../g,s/k/m | Formatted writing of .mcl conformational libraries (see update 020327) has been removed again to avoid confusion of file types. Writing and reading binary files now also works under Windows. To transfer conformational libraries between platforms the .cif format can be used. |
020606 | srf/d/i | This new option allows to exchange inside and outside of a surface. |
020603 | srf/q | Surfaces of the Connolly type can now also be generated for pharmacophore-type entries. |
020603 | MAB | An error in the refined H-bond pattern algorithm has been mended. BUG. |
020531 | Guided Tour | The guided tour 'Building a Small Molecule or a Peptide' has been extended. It now also explains how to deal with the monomer nomenclature of Brookhaven's .pdb format. |
020530 | opt/m | With a new mask option one can give sp2-hybridized acceptors with two lone pairs the possibility to accept three H-bonds. |
020530 | opt/d | On the LINUX platform force-field dynamics did not work. This has been mended. BUG. |
020529 | Guided Tour | A new tutorial 'Protein X-Ray Model Building' is available, which leads through some of Moloc's options in X-ray modeling. It can be found in the advanced topics of the 'Beginners Corner'. |
020527 | MAB | The H-bond pattern algorithm has been improved. Some of the more involved H-bond networks containing water molecules are now treated more realistically. |
020527 | Guided Tour | The example structure of the guided tour, 'Electron Density Maps', located in the 'Beginners Corner', has been changed to the small protein Crambin and the file type of the map to 'XPLOR formatted' (.mpf) to make the example available for all platforms. |
020527 | map/s,i | In order to enable to transfer electron density maps between different platforms, option 's' of the 'map' menu now allows to write a map to a disk file in Xplor-format (.mpf). The previous option 's' has been renamed to 'i'. |
020524 | mch/d/w | The coverage parameter, which was previously restricted to values above two, can now take values from zero onwards. A value of two gives four initial orientations, a value of one simply takes the current orientation as starting pont for the optimization step. A value of zero leads to omitting any optimization, i.e. the similarity value of the given orientation is calculated. |
020524 | .../s/i | Storing several structures of different type on a '.cif' file led in cetrain circumstances to a file which could not be read back correctly. This has been corrected. BUG. |
020524 | map/g | Electron sensity maps in CCP4 format can now be read (default extension .ccp). |
020521 | Guided Tours | The tutorials (guided tours) 'Descriptors for Pharmacophoric Properties' and 'Pharmacophore Descriptors for Sustituents', located in the 'Beginner's Corner' have been finished and adapted to the new features and menu structures of Moloc. |
020521 | Tutorial | A new tutorial 'Pharmacophore Descriptors' has been written. It can be accessed from the Moloc home page. |
020517 | mch/d/h | The menu point has been extended to allow for the calculation of moments of rooted topological pharmacophores. When a table format is chosen, the user can specify to which order the moments will be evaluated. |
020517 | php/w | The menu point has been extended to allow for the calculation of topological pharmacophore moments. When a table format is chosen, the user can specify to which order the moments will be evaluated. |
020517 | Msrfvl | The calculation of topological pharmacophore moments has been generalized. The user now can specify to which order the moments will be evaluated. Thus the parameter -m expects now a number. Values from zero to a maximum of three are allowed. The previous call with -m now corresponds to -m1. An error in the table header of the earlier version has also been corrected: 'Daa' and 'Ddd' were exchanged. |
020514 | lib/d/r,q | Substituent-descriptor generation has been reorganized and augmented by rooted topological pharmacophore moments. |
020514 | mch/s, lib/d | The fragment match menu has been modified and made accessible from the library main menu. When accessed from the match menu, only the matching options are visible (and accessible). When accessed from the library menu all options are available. |
020514 | tpr | In accordance with the reduction of H-bond donor- and acceptor strengths the default threshold for donor- or acceptor agons in topological pharmacophores has been reduced to 1.0 (former value 1.3). This change is effective in many places! |
020412 | Batch Programs | A more explanatory initial description has been added to Moloc's batch programs such that, when started without parameters, they indicate their purpose. |
020412 | Mbcd | In accordance with all other batch programs, the option 'o' has been taken to specify the output file. The previous option 'o' has been renamed to 's' (search options). |
020410 | Msrfvl | A new set of descriptors, 14 topological pharmacophore moments, can now be calculated by setting option 'm'. |
020330 | Tutorial | A new tutorial 'Fragment Positioning' has been added to the beginners corner. It presents an example how to generate positional conformations of a small molecule within a protein cavity. |
020328 | Tutorial | A new tutorial 'Conformation Analysis' has been added to the beginners corner. It presents an example how to generate and analyze conformations of a small molecule. |
020327 | .../g,s/k/m | The Moloc format for conformation library files used to be unformatted. Now there is a IO parameter (libformat) which, when set, writes (and reads) the same information in formatted form. This facilitates the transfer of files between different platforms. For Windows NT the unformatted version did actually never work! |
020322 | Msrfvl | The program has been modified. Every group of quantities to be calculated has to be specified explicitly, otherwise the program does nothing. Some of the switched have been renamed. Two additional quantities can be calculated: 1. approximate surfaces (fast), 2. counts of proton carrying groups. The previous default calculation now requires the command 'Msrfvl -hgd1000'. |
020305 | opt/e/n | The menu for normal mode analysis has been reshaped. Now the user can indicate the number of zero-frequency modes expected for thr system. |
020305 | opt/e/e | The solvation part of the energy evaluation part has been updated. The more recent parameter values for solvation yield slightly modified results. The help text has been extended. |
020304 | mch/d/d,r,a | Selected entries in the cluster analysis are now displayed with bonds in stick representation. In previous versions, half-bond representation was indicative of selection. This collided with the new mode of displaying topological pharmacophore properties of agons. |
020301 | News Flash | When staring up Moloc, important recent modifications apear at the bottom right corner of the display for the first few times the main menu is displayed. |
020215 | MAB | The hydrogen bond-energy has been rescaled (reduced) to correspond to free energies of hydration instead of to vacuum H-bond energies. The old scale can be restored by setting a corresponding flag (opt/m, dTp/o/m). In H-bond strength's the reduction factor is 1.3346, which amounts to a reduction of H-bond energies by 1.78116. |
020214 | srf/a dyn/g Msmab -Hhd Mamber -hd | The atomic charge calculation has been modified to allow for a continuous adjustment of the distribution of atomic hybridization dipol moments. Before the choice was just between distributing them and not to. |
020211 | xnr/e | The generated environment can, optionally, be directly included in the original entry instead of yielding a new entry. |
020206 | opt/e/e | In the utility to evaluate entry energies two bugs were corrected. The angular energy was not always summed up correctly. The solvation free energy missed isolated atoms. In addition, the help text was extended to explain the terms in the solvation energy table. |
020205 | mch/p/v,l,s | Flexible pharmacophore matching, as well as performing all these options on a set of structures has been implemented. Option 'S' has been removed. Instead, choice of any of these options with the shift key pressed indicates, that it is to be applied to a set of structures. |
020201 | mch/p/l,S,o | Pharmacophore matching has been extended to allow, optionally, for a flexible match during which, in addition to the pharmacophore matching function, the moved entries are subjected to MAB force-field restoring forces. |
020129 | mch/s/r | For substituent specific surface calculations topological distance moments have been added. |
020122 | MAB | For several metal atoms covalent bond radii have been added to the force field parameters. |
020122 | .../g/p | When reading .pdb files, selenomethionine residues (MSE) are now recognized and the correct atom type 'Se' is taken. |
020122 | Mamber | This new batch program generates input files (.lib, .dat, .so) for the program AMBER for all organic molecules that can be treated by Moloc's force field MAB. As input .mol2 and .mol (.sd) files, which may contain several molecules, are currently supported. |
020121 | set/j | In addition to writing a file of the atoms of the current set, one can now also simply generate a new entry containing the atoms. |
020121 | opt/e/s | In addition to energy thresholds one can now also set an upper distance threshold for the display of H-bonds. |
020121 | xnr/f | Completing a structure did not work in all cases. |
020115 | dyn/g/a | Input files (.lib, .dat, .so) for the program package AMBER can be generated. |
020108 | xnr/e | In certain cases where the asymmetric unit contains incomplete molecules (which must be completed with option 'f') option 'e' did produce double copies of these molecules. This has been corrected. |
020103 | .../:/o | Dot size of dotted lines come now in three sizes as for dotted surfaces. To change the dot-size of lines this option 'o' has to be chosen with the SHIFT key pressed, otherwise surface dots are modified. |