Step 1: Retrieve an atomic model

Files generally are retrieved with the use of a web browser from the Research Collaboratory for Structural Bioinformatics' Protein Data Bank (http://www.rcsb.org/). You may also retrieve them from RCSB with the use of a file transfer protocol (FTP) program from the RCSB ftp site (ftp.rcsb.org).

The PDB web site (http://www.rcsb.org/) has search capability so you can search for a structure there.

If you have the PDB identification number (e.g. 1PVC for poliovirus type 3, Sabin strain), you can download the coordinates from the PDB FTP site. Use the following procedure to FTP the file from the RCSB FTP site (ftp.rcsb.org). This example is for a command-line FTP program. Your program may differ in how it is started and how you connect to the remote site.< /P>

   >FTP [cr]  (run your FTP program)

   >open ftp.rcsb.org [cr]  (connect to the RCSB FTP site)

   user>anonymous [cr]

   password>your full e-mail address [cr]

-Enter the directory for compressed PDB files.

   >cd /pub/pdb/data/structures/all/pdb/ [cr]

-Download the desired file to your disk.

   >bin [cr]    (tells the computer the file is binary)

   >get pdb1pvc.ent.Z [cr]              (for example)

Once you've downloaded the file (e.g. pdb1pvc.ent.Z), use the "uncompress" pr ogram to convert the file to its ascii form (e.g. pdb1pvc.ent).

Pseudo-atomic models can also be used to make low-resolution density maps. See Belnap et al. (1998) for a discussion of pseudo-atomic models.