Based on the need for more interactive software to view neuron data (obtained by Electron Microscopy), we have begun to adopt QMView to view multiple datasets of neuron data. Researchers within the Martone/Ellisman group use the "SYNU" (SYNthetic Universe) file format to store polygons representing volume data of neuron structures. Normally QMView takes grid data and calculates polygons representing iso-surfaces. In this instance, the polygons have already been calculated. A perl script was written to extract polygons from the SYNU files and make a file which QMView reads. The data in each SYNU file is treated by QMView as a separate object and may, like more then one molecule, be manipulated separately, or together. Data from two SYNU files are shown above. Another element of visual analysis that they would like to pursue is to be able to click on a segment of the structure and identify it. This can be implemented within QMView in an analogous fashion to clicking on an atom to display a label.

NwV Virus data from electron cyro-microscopy

In collaboration with Jack Johnson and Padmadja Natarajan

Jack Johnson's group at TSRI has expressed a desire to view conformational changes in a virus. They have electron microscopy data of individual conformations, but they would like to view continuous motion. This work involves:

1. Adopting QMView to read the data files.

2. Develop software to produce a smooth animation (e.g. morphing).

Step (1) is nearly finished. The data is in the CCP4 (Computational Crystallography Project Number 4 (project of the UK Science and Engineering Research Council)) file format. This data is grid data that must be converted into polygons in analogy to grid data obtained from a QM program representing electron density or MO's. Images have been obtained with QMView (see above). All but one image is correct we are working on that (probably due to incorrect axis choice).

Step (2) is more challenging, due to the fact that the grids for each data set are a different size and/or scaled differently. This is something that can be worked out.

DataMining Facility in Conjunction with the PDB (Bourne)

PDB Queries:

In order to facilitate extraction of ligands coordinate data from the PDB, we have started to put in data-mining facilities into QMView. As a first step, we have

PDB querying

implemented an option in QMView whereby the 4 character PDB code is entered as well as a ligand residue name in order to display the PDB data, and highlight the chosen ligand, and extract the ligand data. For the above example, the display of the entire structure is:

E. Coli. glycerol kinase mutant with bound ATP (ATF is an ATP analog with Flourine attached)

The protein can be removed leaving the two ATF ligands. They can then be protonated (in progress) and a GAMESS file can be written

Naked ligands/protonated