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Date Menu Option Description of Change 971218 .../s/i The cif file can now contain atomic charges. They are .../g/i automatically stored onto file, and read when available. 971217 cnf/c/b Background entries are now stored as .b.cif files in order to retain any possible polymer information (to speed up the preparatory phase of the force field calculation). 971217 pca/c/s Peptide vectors and C-beta are correctly displayed when viewing the results of a fragment search. BUG 9712xx The manual for Moloc has been updated. The chapters after the introductory one are just repeating the online help texts. Consequently, most online help have been completed and been brought up to date. 971127 mch/s Fragment recognition improved. BUG 971110 Picking in Molox has been amended. BUG 9711xx opt/e/n Normal modes of deformation (not vibration) can be calculated and displayed. 9711xx Online help has been augmented by a search option, which is activated by selecting the question mark with the control key pressed. Search covers just the current menu. 971015 opt/e/a Atomic hybridization dipoles are printed when atomic charges are calculated. 971015 srf/a The calculation of atomic point charges has been standardized to utilize the new force field with a special parameter set to account for the omission of atomic hybridization dipoles. 971014 geo/w/m The electric dipole moment of a molecule with given atomic point charges can be calculated. 971014 geo/w/a A threshold can be set for the interpretation of geometry data of sets (see geo/w/g). 971014 geo/w/g The comparison of geometry data of two sets of atoms has been generalized to deal with one- and two-atom sets as well. 971013 mch/s Fragment recognition improved. BUG 971013 pca/p/i List of calculated data fixed. BUG 971007 .../g/p The Naming of the N eta atoms of arginin has been changed to conform with the UPAC rules. 970926 opt The valence angle bending potential has been modifies for the case of large angle values, to yield a somewhat higher barrier. 970926 dTp/k Adding explicit hydrogens may optionally exclude aliphatic carbon atoms. 970923 .../s/m Writing and reading of .mab files now includes atomic charge values. 970923 opt/m The case of working with input charges has been put on a somewhat more systematic footing. 970923 mch/s Substructures of a set of entries can be matched on top of each other. Recognition of the (connected) substructures is automatic. The multimatch algorithm is used. 970922 mch/m/h For pairwise matching of two Calf strustures, pairs of corresponding Calfs can be specified by reading a file of the format used in homology building. 970922 opt/c/l List for positional constraints shows upper and lower flag. 970918 pca/p/p The scaling factor for the RSCC calculation has been pca/p/i modified. 970918 xnr/j Chosen color is now accepted. BUG 970917 pca/p/p/t The sliders for setting the thresholds now also show the pca/p/i/t average and rmsd values for user information. 970917 pca/p/p/g Access to the geometry tool has been inserted in the menu. 970917 srf/c The surface coloring option has been moved to the entry display option .../e/c and H-bond and charge information are kept on the .jkl surface files. 970916 .../g/k/p Multiconformer structures on .pdb files can be read as a Moloc conformation library. This is usefull for solution NMR structures in which the conformations are indicated by the keyword MODEL. 970913 pca/p/p/p In the residue scan menu a list of the actual values of the calculated quantities can be printed. 970821 geo/a Text of up to 127 characters can be attached to an atom position. 970808 opt The half width angle of H-bond donor has been modified to 46 degrees. Acceptors have 60 degrees. 970808 php/g Hypotheses out of Catalyst can be read into a Moloc pharmacophor via a file of .filtlog format. 9708xx The graphics part of Moloc has been rewritten using the more modern OpenGL graphics language and the X-windowing system. Thus, at present two executable files exist: Moloc, which performs best on older SGI machines, and Molox for the newer machines. Molox can also be used from PC's over the network when a OpenGL-capable X-emulation, such as ReflexionX is available. This is a major modification and we expect to have to deal with straightening out activities for some time. 9706xx opt The H-bond strengths in the force field MAB have been improved by applying a modified preparatory calculation (JCAMD in press). This is a major change and uncovering of bugs and other modifications are expected to go on for some time to come. The old force field can still be used, in particular in cases where obvious errors show up. In the course of this modification new features are available, such as the examination of pi-orbitals (opt/e/o) ore the examination of donor and acceptor strengths of polar atoms (opt/e/w/a). 97xxxx dyn/g/g GROMOS topology files can be written in the new GROMOS96 format. 97xxxx pca/p/i,p Scan options for residues (p) and isolated atoms (i) have been unified and based on the same calculation. The quantities of interest are only calculated once unless the user specifies otherwise. 97xxxx pca Geometry (g) and forge (f) options have been introduced here to facilitate repeated use of options m, r, and p. 97xxxx pca/u Full (all atom) proteins can be updated from a C-alpha structure also in case this has been augmented in the Calf builder. For the exact procedure consult the online help. 97xxxx When starting Moloc with a file name on the command line, file reading can be governed interactively by adding the flag -i (see by starting Moloc -h). This can be usefull when starting Moloc automatically for e.g. a .pdb file as may be the case in WWW applications. 97xxxx mch/t/f In addition to the old Moloc .trf format, transformations can be written and read in 'O' format (file type .tro). This latter is the default. 97xxxx dyn/g/t Writing of TNT geometry files has been modified (removing kommas) to obey TNT-convention. 97xxxx mch/d/r A previously performed similarity calculation stored on a .sml file can be reexamined by reading the file. The corresponding entries must be read in beforhand (e.g. from a .mab file stored under mch/d/f) and are then assigned automatically. 97xxxx mch/d/d/g A previously stored selection (.smi file) can be retrieved mch/d/r/g for repeated examination. No additional structures are mch/d/a/g entered into Moloc, but the old marks for selected entries are replaced by the new ones indicated on the file. 97xxxx dyn/y Polar hydrogens can be added ito conform with the hydrogen- bonding pattern as calculated by the MAB force field. This includes the conformation of hydrogens which are not engaged in a bond themselves, but have restrictions because a lone pair accepts a hydrogen bond. 97xxxx srf/e Option is also effective for Connolly surfaces. 97xxxx frg/k Coordinate transfer from one entry to another can also be specified residue- and entry-wise. 97xxxx set/j In addition to .jkl files a set can be sored as a .pdb file. 97xxxx mch/r Several entries can be specified to be relocated at once. 97xxxx frg/h,l Picking the auxillary peptide display (pepdide planes, side chains) is disabled. BUG 97xxxx xnr/j Immediately updated equivalent cristallographic positions also show atom markers and -labels. 97xxxx pca/c/s/d/+ The results of the loop search can be viewed by cycling forwards and backwards through the hit list. 97xxxx pca/c/s/d,e Actual sequences of segments found in the database are pca/m/s/d,e given in screen help 97xxxx frg/l Actual phi-psi values are indicated in menu header when turning peptide links.