Biomedical subjects

G Schaftenaar

Publications and source records attributed to G Schaftenaar.

3 recordsLinked to original sources

PubMed2000

The effect of isodensity surface sampling on ESP derived charges and the effect of adding bondcenters on DMA derived charges.

The effect of sampling the electrostatic potential around a molecule on the quality of electrostatic potential derived charges is investigated. In addition, the effect of the number of expansion sites in a Distributed Multipole Analysis (DMA) on the quality of charges fitted to the DMA derived electrostatic potential is investigated. Sampling on constant electron density surfaces gives a better fit between the quantum mechanical potential and the potential derived from the fitted charges, compared to sampling on a van der Waals surface composed of intersecting spheres. The fit between the electrostatic potential derived from point charges and the quantum mechanical potential becomes poorer with increasing quality of the employed basis set. The inclusion of bond-centers into the calculations improves the fit between the Quantum Mechanical (QM) electrostatic potential and the DMA derived potential. The number of expansion sites needed for an accurate approximation of the QM electrostatic potential increases with increasing quality of the used basis set.

Models, Molecular↗

PubMed2000

Molden: a pre- and post-processing program for molecular and electronic structures.

Molden is a software package for pre- and postprocessing of computational chemistry program data. Interfacing to the ab initio programs Games-US/UK and Gaussian and to the semi-empirical package MOPAC is provided. The emphasis is on computation and visualization of electronic and molecular properties but, e.g., reaction pathways can be simulated as well. Some molecular properties of interest are processed directly from the output of the computational chemistry programs, others are calculated in MOLDEN before display. The package features different options to display MOLecular electronic DENsity, each focusing on a different structural aspect: molecular orbitals, electron density, molecular minus atomic density and the Laplacian of the electron density. To display difference density, either the spherically averaged atomic density or the oriented ground state atomic density can be used for a number of standard basis sets. The quantum mechanical electrostatic potential or a distributed multiple expansion derived electrostatic potential can be calculated and atomic charges can be fitted to these potentials calculated on Connolly surface(s). Reaction pathways and molecular vibrations can be visualized. Input structures can be generated with a Z-matrix editor. A variety of graphics languages is supported: XWindows, postscript, VRML and Povray format.

Computer Simulation↗

PubMed1996

A Tcl-based SRS v. 4 interface.

A new SRS (Sequence Retrieval System) user interface has been developed for SRS v.4. Key features are the support of simple character-oriented (ASCII, VT100) terminals by coding in Tcl augmented by some dedicated Curses calls, support of graphics terminals in an X-Windows version by using the Tk extension to Tcl, and support of a client/server environment by using the TDP extension to Tcl. The Sequence Retrieval System (SRS) is a powerful tool for the fast extraction of information from flat file libraries (Etzold and Argos, 1993) and has rapidly established itself as a major research instrument for the bio-informatics community. Internally the system employs a query language, which is user accessible through either a command-line user interface, 'getz', or a more user friendly, character-oriented window interface. For SRS versions up to release v. 3, this window interface supported VT100-compatible terminals. Because of major changes in the underlying SRS libraries, the v. 3 interface became fully incompatible with the most recent version of SRS (v. 4.x). Thus the many users with only a simple terminal/terminal emulator connection were either deprived of access to SRS, or were forced to use the ASCII WWW client LYNX. This prompted us to develop a character-oriented SRS v. 4 window interface with the look and feel of its SRS v. 3.1 predecessor and coded to be as library independent as possible to maintain compatibility with future SRS releases. In addition, some 'extensions' were coded to widen the applicability to graphics terminals and to a client/server environment. At the time of preparation of this paper, the SRS interface described had been implemented in one form or another on most EM Bnet nodes and on all the platforms given in Table II. The code has been stored at the EMBL in Heidelberg, where it will be available, with installation instructions and scripts, as part of the SRS distribution.

Computer Graphics↗