To see a molecule in Protein Explorer (PE), you must first
choose an atomic coordinate file (often called a
that contains the 3D structure of the molecule.
(Protein Explorer cannot calculate the 3D structure of a protein from
the amino acid sequence -- see
Nature of 3D Structure Data.)
Each PDB file has a unique 4-character identification code.
Examples: 2HHD (hemoglobin), 1BL8 (potassium channel).
If you don't know the PDB ID code you want,
see below to find it.
After you find
the PDB code you want, enter it
If you want to compare two PDB files ("molecules")
side by side,
enter two PDB ID codes in the slots below, and click the
How To Find Molecules
Published macromolecular structures are archived
at the Protein Data Bank (PDB).
Search for the
molecule you want, and then click on the Protein Explorer link
built into the search result page. Or, notice the PDB code, and
enter it in the slot above.
If you are offered PE version 2.0 or 1.0,
select version 2.0!
is an advanced
PDB searcher at the Weizmann Institute
with some capabilities not found in the RCSB search interfaces.
The PDB file for your molecule may contain only part of it. For
example 1HHO contains only half of
the hemoglobin tetramer. Or it may contain multiple copies when
you only want one. After you see the molecule in Protein
Explorer, use the Molecule Information link, Mol Info,
to get a single whole molecule, or just one chain.
These don't have direct links to PE -- use them
to get the PDB code, then enter it in the
PDB at a Glance
is a convenient browsable list of molecules, arranged in
categories like enzymes, membrane-associated proteins, nucleic
acids, etc. etc. Use it to get the PDB code to enter in the
You can create web pages containing hyperlinks that prespecify molecules
to be displayed in Protein Explorer or Comparator.
The PDB files can come from the Protein Data Bank or any other server,
or your local hard disk.
The simplest format for a hyperlink, for example for PDB ID code 1d66, is
PE automatically gets the PDB file matching the prespecified PDB ID code
from the Protein Data Bank server.
For two molecules side by side, for example calcium:calmodulin with
and without bound peptide:
You can download
PDB files to keep on your computer's local disk.
The most reliable
way for novices to download PDB files is by using
running "bare" PE, you can use the Browse button (on the
"Different Molecule"/"Load Molecule" page) to locate
and load saved PDB files from your hard disk.
"Bare" PE remembers the last ten files you have
loaded at its "Load Molecules" page,
and offers to recall them from a pick list.
Or you can make an HTML page containing
to your favorite molecules.
If you know the PDB identification code(s), or have the PDB files downloaded
and saved on your local hard disk, or you have loaded the molecules of interest in
a recent session with PE, you can tell PE what molecule(s) to display
after you have entered either the