When you click on a Research Group link, you will be presented with a password dialog box that asks for the research group name and its password. (To get your group's password, call Pat Carroll at 8-3505). Once you've entered the password, you will be transported to an index page that displays structural drawings of the compounds for which X-ray data are available. Clicking on one of these drawings will get you to a page that displays a java frame in which that molecule will be displayed. This visualization of the molecule can be rotated in real time and can be displayed in several formats (play with the pop-up menu accessible by a right-mouse click on a PC or a control-mouse click on a Mac!)
Below the java frame are clickable links to download the PDB file and the CIF file.
The PDB file can be read by
Chem3d or
Rasmol (Rasmol is a freeware molecular visualization program that can be
downloaded from
www.umass.edu/microbio/rasmol/getras.htm) or the
Jmol application.
The CIF file is required by most journals as supplementary information
for any published X-ray structure. The CrystMol program can be used to visualize the molecule and to
perform "crystallographically-correct" molecular geometry calculations
(bond distances and angles, hydrogen bonds, least squares planes, dihedral
and torsion angles, etc. including estimated standard deviations). CrystMol can be
downloaded from www.crystmol.com (there are versions for both
Mac's and PC's). We have a department-wide license for CrystMol that can be obtained from Pat Carroll.
At the bottom of the page is a link to a second page that allows the user to investigate the unit cell and build a packing diagram. (This facility was added in May, 2007 so earlier structures do not have this capability).
If you have any questions about these pages call (8-3505) or e-mail (carrollp@sas.upenn.edu). Suggestions for improving and expanding these pages are welcomed!