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Updates 2003

Updates 2003

DateMenu-OptionDescription of Change
031229frg/l The turning of peptide links has been generalized to also work on all-atom peptides.
031229pca/c/m Chi-angles of amino acids are selected depending on secondary structure (phi,psi-angles) when building new proteins (most likeky rotamer).
031222frg/h Driving chi-angles has been extended to all-atom proteins. Furthermore, the Ponder-Richards rotamer library has been modernized to the penultimate one. Since some residues have rather lengthy lists of rotamers, backward toggling has been added (Alt-key).
031217xry/m,n Option pca/p/m (modifying full protein structures) has also been installed in the X-ray utility menu 'xry' as option 'm'. The previous option 'm' (modify Calf structure) has received the letter 'n'.
031217.../s/p Residues that had been changed to another type did not reveive the corresponding three-letter code when saved to ai .pdb file. This has been changed. BUG
031211frg/j In the menu to handle alternate conformations, a new option, 'm', has been introduced. It allows to modify the set of atoms that have several conformations. In addition, a few minor modifications have been made.
031204xnr/u The ring-shape analysis utility has been extended.
031201.../g/i Half bond coloring was overwritten when reading a .cif file. This has been corrected.
031127frg/j
pca/,
The alternate location utility has been extended by two options: 1) insertion of new locations by picking an atom (option 'p'); 2) toggle display of all locations (option ','). A picking version of this last option can also been invoked in 'pca/,'. Finally, some bugs have been fixed.
031124srf/d/c When coloring a surface to display the electrostatic potential or field strength, the contribution of atomic quadrupole moments can now be included.
031119Msrfvl -q This new option allows to characterize the position of atoms specified through a given atom type (e.g. He) with respect to the rest of the structures (template). The output contains the rms extension of the template from its centroid, given along its principal axes. For all specified (He) atoms polar coordinate values with respect to this principal axes coordinate sysstem are given. The option works only in redirect mode.
031119xnr/u A long-forgotten ring-shape analysis tool has been reimplemented. It has also been extended by a cluster analysis option.
031119.../g,s/p
frg/j
Handling of alternate locations (reading from and saving to .pdb files) has been implemented. Which one of these locations is seen (and are possibly modified) in Moloc is governed within the alternate-location management menu 'frg/j'. This menu also allows to introduce new alternate locations.
031117pca/s The Fourier analysis tool of protein sequencies has been restructured. Help texts have been added.
031112.../g,s/i Library specifications are now also stored to, and recovered from .cif files.
031106lib/c
Mdck
For molecules with many rotatable bonds the initial poses generation has been accelerated.
031106Mngsd The new option 'f' allows to specify a file containing the names of the structures that are to be extracted.
031105Mfltr The new flag '!' yields the a file of the eliminated structures instead of the surviving ones.
031105lib/f
Mfltr
The verbose output of the filter routine has been improved.
031028Mol3d Protonation did not work in some cases; his has been fixed. Note that the options 'l' and 'p' may be incompatible (see help).
031027lib/c
Mdck
A new option parameter 's' has been introduced. If set to a non-zero value, the docking program runs in superposition mode; i.e. the 'ligamds' are superimposed onto the target structure, using pharmacophore features for estimating the quality of superposition.
The previous option 's' (softness of potentials) has been renamed to 'y' (yielding).
031022Mol3d If the 'worry' parameter 'w' is given a value larger than 5, the initial (2d) coordinates are ignored and a 'ab initio' conformation is generated, utilizing the algorithm of the program Msmab.
031022Mol3d The initial randomization of coordinates has been modified to improve the final conformations.
031014Mol3d The program has been modified to yield true force field mimima in all cases. The worry parameter has been redesigned such that small positive values (instead of previously negative ones) lead to little disturbance of coordinates (no disturbance for a value of 0).
030910.../g/p Reading and storing non-standard amino acids in .pdb format has been improved.
030901Mdck A new option '-y' enables handling of .mol2 files.
030901Mdck The program now accepts structures with explicit hydrogen atoms.
030820.../+/w This new option will remove the water molecules from all specified entries.
030819Msrfvl In the redirect mode the output has been modified. Each group of properties now appears under a sepatate data tag in the .sd file. The tags are specified in the help text.
030818Mol3d Setting the flag '-l' (keep only largest component) now leads simultaneously to replacement of explicit hydrogens by silent ones (united atom approximation).
030818lib/c
Mdck
Similar poses can now be eliminated by specifying a minimal rmsd of atomic coordinates (flag '-f' in Mdck).
030815php/m Generation of a pharmacophore from an all atom structure has been enhanced in two ways: - Atoms can be specified, which are discarded when pharmacophoric agons are generated. - For all hydrophobic agons an axis is calculated (the axis of largest normal extension). Agons with large aromatic content are automatically specified as ring-aromatic with the calculated axis as ring normal. For other hydrophobic agons the direction is also kept for the case, that the user decides to respecify them as ring-aromatics.
030815php, Mbcd An additional type of pharmacophore agons, "ring-aromatic", has been introduced. At present it mainly serves to enable the generation of Catalyst hypotheses with the corresponding type of features. Within Moloc they are treated like the other hydrophobic agons. However, they are displayed as a ring segments of spheres, and the directions of the ring axes can be changed in the same whay as the directions of polar agons.
030814Mdck The batch program for docking has been modified to allow for multiple-pose output.
030813php/c Reading of .chm files has been revised.
030813Msrfvl A new option '-t' yiels atom typing. For each atom the state of hybridization, the hydrogen-bond donor- and acceptor strengths are calculated. The option works only in redirection mode (together with option '-r').
030717Mol3d A new option -l allows to desregard all disconnected components of a structure except for the largest fragment. Atom related data stored in the .sd file may loose their proper order in this process. However, formal charges in the field "M CHG" are properly updated.
030717lib/f, Mfltr Filtering for formal charges has been improved.
030717Msmab
Mtprgn
In these programs, structure protonation has also been updated to enable use of the ACD program for calculating pKa values.
030702.../s/l When storing structures in .tdt format, the user is asked whether new SMILES codes need to be generated. This is the case, when changes in molecular topology have been performed.
030626mch/m/w When matching C-alfa structures, this option allows to write an alignment file on the ground of geometrical criteria.
030626lib/e A new option in the evaluation of entries has been added. It writes (prints) for each specified entry a list of atoms together with their H-bond donor and acceptor strength. For non-polar atoms the first number is negative and characterizes the state of hybridization while the second number is zero.
030624.../l Transfer of display features from one entry to a whole library of entries now also includes the color. Only features that have been altered are transferred.
030624mch/s/s
lib/d/s
Under certain circumstances the recognition of substructures failed. This has been corrected. BUG.
030618set/d Distance-related set generation has been augmented by two options which serve to weed out atoms of the distance set which do not contribute to cavity definition.
030618lib/b/e/q
lib/b/e/w/q
When the browse menu is called for a library, it is possible to examine putative H-bonds between the molecule under examination and a receptor cavity given only in pharmacophore representation. This option cannot be called from the 'opt' menu directly.
030618php/n Three types of entries: pharmacophore-, force-, and positions entries are handled in the php menu. Correspondingly, when generating a new entry one has now to specify its type.
030618lib/c
Mdck
All items in this list that date of today are related to the new possibility in Moloc of docking small molecules into a receptor cavity. With it come a set of new options which allow for necessary preparation activities. A tutorial in the 'beginners corner' presents a test example. Mdck is the batch version.
The cavity can be given in atom- or pharmacophore representation.
030616.../g/i When reading backbone structures of DNA (RNA) the monomers lost the information on their type. This has been corrected.
030616mch/d/d,r,a/d Entry data can be displayed branch-wise (option 'd').
030616Mngsd A new option 's' allows to write non-numeric data (character strings) in a table.
030616Mfltr This new program makes the filtering function (menu lib/f) available in bach mode. It works on .sd files (also in piping mode).
030616lib/f The specification for filtering entries with respect to formally charged atoms has been changed (see help in corresponding slider popup).
030616lib/f The specification for filtering entries with respect to formally charged atoms has been changed (see help in corresponding slider popup.
030602.../:/r Rocking- movies can be produced as a sequence of bitmap image files. When quitting the sliders for rocking-parameter setting the user is asked whether such files should be created.
030602.../:/i Bitmap images can now also be written for Windows.
030527Mol3d
Msmab
Mtprgn
Mtprmp
Structure protonation can now in addition pe performed with the pKa program of ACD. This option is restricted to the SGI platform, where the program is installed. To protonate the structures of an file tst.sd, issue the command 'Mol3d -m1 -p4 -P7 tst.sd'. The result file tst_3d.sd will contain the structures in a state of protonation which the ACD program thinks they should have at pH 7.
030522.../:/r Display rocking parameters can be set here: direction of rotation axis, range and stepsize. Pressing Alt 'r' yields a single rocking event. Alt 'x', 'y', and 'z' lead to rocking about the corresponding axes. The menu item to write .rgb files has been renamed to 'i' (bitmap image)
030521Mol3d A new option, -n, has been introduced which provides the possibility to specify a tag from which the molecular names are taken. The corresponding names then also appear in the first line of each structure. The command 'Mol3d -m1 -n NAME test.sd' will just produce a new file, test_3d.sd, in which the names given under the tag 'NAME' also apear in the first lines. The same feature works in other programs in which a name tag can be specified.
030520MAB The H-bond pattern algorithm has been improved.
030514opt/e The examination menu has been reorganized. Examination of attractive vdW interactions (option 'k') is now reached by choosing option 'r' with the SHIFT key pressed. Likewise, 'q' was moved to SHIFT 'c'. 'q' will be used for a new option (examination of H-bonds to a pharmacophore) which is still under development.
030508lib/d/t The option has been modified to arrange the fragment atoms in all structures such that they will appear first when the structures are written onto file. The previous functionality, deleting the fragment atoms, is now secondary (with SHIFT key pressed).
030508lib/f Libraries can be filtered with respect to number of atoms with positive and negative formal charge.
030430lib/f Libraries can be filtered by the number of rotatable bonds.
030415opt/e/g/t Torsional potentials about a rotatable bond can be displayed.
030331lib/h A tool to generate histograms with bin-wise structure examination has been implemented.
030328sliders Header and help possibilities of sliders have been augmented.
030326Mngsd This new program provides various management facilities for .sd files.
030318Mol3d New options '-p' and '-P' have been introduced to enable adjustment of Hydrogen counts of the atoms as determined by a specified pKa calculation methode. The previous option '-p' (principal-axes transformation and centering onto the origin) has been renamed to '-c'.
030317Mtprcnt An additional table row lists the maximum topological distance encountered in the pharmacophores of each column.
030317Msrfvl The flags of option '-w' now also aply to option '-b'.
030311Msrfvl With the new option -b the two-point agon-type correlation functions are calculated in distance bins.
030228dyn/y
dTp/k
Naming of explicitly attached hydrogens has been improved.
030207Mamber
dyn/g/a
To corresponding atoms of identical fragments the same atom types are now assigned.
030205Msrfvl In addition to the 5 geometry parameters, written when the flag '-g' is set the molecular weight is now also printed.
030123Mamber
dyn/g/a
Writing of Amber parameter files has been generalized to also treat multi-fragment entries.
030123Msrfvl A new parameter, -w, allows to set special switches for the calculation of topological pharmacophore moments.
030123Msrfvl A new parameter, -x, allows to specify the maximum number of heavy atoms allowed.
030123srf/c,q For calculated surfaces the contribution of polar atoms is given in addition.
030123Mphmch This new batch program allows to perform pharmacophore matching of a set of structures onto a target structure. Similarity values are listed in a table file, and a new structure file is written in cases where an actual match is specified by the user.
030123lib/b A new browsing option is provided which allows to simultaneously step through the entries of several sets of structures. To access this option 'b'-selection must be made with the shift key pressed.
030110xtl/c Help text has been added to the menu items for the generation of unit cell displays. Furthermore, when an entry is repositionned during cell generation from scratch the repositioning transformation is kept so that additional entries may be moved with the same transformation (options mch/t/c and mch/r).
030110.../+/z Crystal information of entries can be removed which may be necessary for force field calculations with periodic boundary conditions.
030110opt/m Periodic boundary conditions can be applied to force field calculations.
030107.../g/l
dTp/m
When reading SMILES code, some cases of cyclic structures ended up with incorrect H-counts. This has been corrected. BUG
030107MAB Automatic recognition of electron counts in PI-systems has been improved.