C371 Exercise 5: Molecular Visualization and 3D Searching

Fall 2004
Updated: 8 November 2004

1. Use the Cambridge Structural Database to work through Tutorials 4 (3D Substructure Search) and 6 (Pharmacophore Search) on computers 5-9 in the Chemistry Library at IUB or in the IUPUI Department of Chemistry Computational Molecular Science Facility.

[ ] I successfully completed the assigned tutorials.

2. Download the file 1GQT.cif.

Use the Mercury program to view the file, but uncheck the box to Show hydrogens. (Mercury is available on computers that have the Cambridge Structural Database or as a free download at:

Did it work? If not, why?

Now view the file in ChemOffice's Chem3DPro. (It is NOT on the STC computers.) [Note that you can download the ChemDraw Ultra program to your own computer (not an STC computer) by creating a CambridgeSoft user account and installing ChemDraw Ultra (which includes Chem3DPro) at:]

Choose the model type "Ribbons," then, under the Tools menu, magnify the object until you can clearly see the small molecules depicted. Grab the rotate tool in the left column (arrow with a circle around it), and rotate it around all three axes.

While in the program, note the many options to work with the molecule.

[ ] I have completed this part of the assignment.

3. Not long ago a subscriber to CHMINF-L had a question about the CAS Registry Number for a compound for which he had only the SMILES code. It turned out to be 4-(4-pyridinyl)-bezeneamine (RN: 13296-04-3). Find the compound using SciFinder Scholar, and print out the full record for the compound.

Return to the previous window in SciFinder Scholar, view the molecule in ViewerLite (hit the water molecule icon), and save the file from ViewerLite as an MDL MOL file.

Using the Cambridgesoft ChemOffice program Chem3DPro, open the file.

Did it work?

4. Using the SMILES code NC1=CC=C(C2=CC=NC=C2)C=C1 connect to CORINA at:

Input the SMILES code, give it the identifier (name) corina_bezeneamine, and Generate the 3D structure. Does it look correct on your screen?

Now save it as a WebLab Viewer Pro sdf type. Open Accelrys ViewerLite and view the molecule. Does it look correct now?

5. Read the brief article in C&EN on 3D models produced with Rapid Prototyping Technology. See:

It uses PDB (Protein Data Bank) data to create the model of biomolecules (a 3D model that you can hold in your hands) by means of 3D printing technology, This web page has pictures of the products:

[ ] I have read the article and looked at the models.