1. Number of released entries
Year

2. Growth of Molecular Complexity
Number of Structures Containing that Number of Chains
Number of Chains
Year

3. Challenges in visualization of complexes and the PDB
HEADER COMPLEX (ACETYLATION/ACTIN-BINDING) MAY HLU
TITLE STRUCTURE OF BOVINE BETA-ACTIN-PROFILIN COMPLEX WITH ACTIN
TITLE 2 BOUND ATP PHOSPHATES SOLVENT ACCESSIBLE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BETA-ACTIN;
COMPND 3 CHAIN: A;
COMPND 4 MOL_ID: 2;
COMPND 5 MOLECULE: PROFILIN;
COMPND 6 CHAIN: P
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS;
SOURCE 3 ORGANISM_COMMON: BOVINE;
SOURCE 4 ORGAN: THYMUS;
SOURCE 5 MOL_ID: 2;
SOURCE 6 ORGANISM_SCIENTIFIC: BOS TAURUS;
SOURCE 7 ORGANISM_COMMON: BOVINE;
SOURCE 8 ORGAN: THYMUS
KEYWDS COMPLEX (ACETYLATION/ACTIN-BINDING), ACTIN, PROFILIN,
KEYWDS 2 CONFORMATIONAL CHANGES, CYTOSKELETON
EXPDTA X-RAY DIFFRACTION
AUTHOR J.K.CHIK,U.LINDBERG,C.E.SCHUTT
REVDAT OCT-97 1HLU 0
JRNL AUTH J.K.CHIK,U.LINDBERG,C.E.SCHUTT
JRNL TITL THE STRUCTURE OF AN OPEN STATE OF BETA-ACTIN AT
JRNL TITL A RESOLUTION
JRNL REF J.MOL.BIOL V
JRNL REFN ASTM JMOBAK UK ISSN
Challenges in visualization of complexes and the PDB
Visualization workshop, October 2003

4. What is PDB’s role in molecular visualization?
Coordinate files
of molecules
Visualization
software =
Visualization
of molecules +

5. What is PDB’s responsibility with respect to molecular visualization?
providing complete & correctly annotated coordinate files in multiple formats (PDB, cif, XML)
providing links & explanations for visualization
software =
visualization for user community – general users, researchers, annotators, students, educators, databases, bio-informaticians +

6. The PDB format The mmcif format
JRNL TITL COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF JRNL TITL 2 RECOMBINANT HUMAN H AND HORSE L FERRITINS AT HIGH JRNL TITL 3 RESOLUTION JRNL REF J.MOL.BIOL V JRNL REFN ASTM JMOBAK UK ISSN
The mmcif format
_citation.id primary _citation.title
;Comparison of the three-dimensional structures of recombinant human H and horse L ferritins at high resolution. ;
_citation.journal_abbrev J.Mol.Biol. _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher ? _citation.pdbx_database_id_PubMed
mmCIF: macromolecular Crystallographic Information
File
This is an extension of the Crystallographic Information File (CIF) data representation (used for describing small molecule structures) to describe macromolecules.

7. Complete and correctly annotated coordinate files
Do PDB files conform to uniform standards?
Yes, Remediated mmcif files are available. They can be converted to PDB format using CIFTr (This application is available at
Do PDB files contain coordinates for the complete biological unit?
Yes, both coordinates and pictures of the biological unit of all PDB files are now available.

8. What is a biological unit?
PDB has coordinates of molecules determined by:
X-ray crystallography
NMR
Electron microscopy
Theoretical modeling
Primary coordinate files for crystallographic structure generally contain one asymmetric (unique) unit.
The biological molecule (also called a biological unit) is the macromolecule that has been shown to be or is believed to be functional. This could include one, a part of or multiple asymmetric units.

9. Concept of the biological unit
Biological unit could include one, a part of or multiple asymmetric units.

10. Downloading biological unit images/ coordinate files from the PDB
PDB ID 1AEW
Information for constructing the biological unit is contained in remark 350 of the PDB file

11. Visualizing the biological unit
Some visualization tools fail to duplicate the secondary structure records for symmetry related molecules in the biological unit
Biological unit of 1AEW
Viewed in RasMol

12. Large macromolecular assembly 1: Viruses
For viruses, usually the coordinates of the icosohedral asymmetric unit are deposited to the PDB. Transformation matrices for generating the complete virus are also provided.
Sometimes additional matrices are provided to generate the icosohedral asymmetric unit from the given coordinates 5 3 2
Virus particles have high symmetry (5, 3, 2)

13. Generating the biological unit of a virus
Coordinates in crystallographic
Symmetry axes
Coordinates in icosohedral
Symmetry axes
Conversion matrix
Asymmetric unit
NCS applied
Asymmetric unit
NCS not applied
Asymmetric unit
Recipe &
matrices 60
matrices
Crystallographic
Symmetry
operations
Biological unit

14. Virus: problems and solutions
Problems: - matrices for generating the biological unit?
- improper nomenclature of the 60 matrices for generating the icosohedral virus particle?
- placeholder for the NCS matrices for completing the icosohedral asymmetric unit ?
- conversion matrix between crystallographic and icosohedral axes?
Possible solutions: - uniform representation of matrices for generating the biological unit?
- change in the nomenclature of the 60 matrices for generating the virus?
- conversion matrix between crystallographic and icosohedral axes always available?
- other?

15. Large macromolecular assembly 2: Ribosomes
The current PDB format can hold:
a maximum of 99,999 atom records, and
upto 62 different polymer chains.
Since there is no way to represent structures that exceed either of these restrictions in a single PDB file we have divided such structures into multiple PDB entries.
Although this is not a perfect solution, we have done this to support existing software that rely on current format.
The mmCIF/ XML format has no such restrictions.

16. Ribosomes 1GIX: Small subunit of the ribosome
1GIY: Large subunit of the ribosome

17. Ribosome: problems and solutions
Problems: restrictions in the PDB file format?
Size of file?
Scaling?
Docking?
Visualization of nucleic acids?
Possible solutions: use of mmCIF/ XML format?
better way to represent nucleic acids?
other?

18. What is PDB’s responsibility with respect to molecular visualization?
providing complete & correctly annotated coordinate files in multiple formats (PDB, cif, XML)
providing links & explanations for visualization
software =
Visualization for user community – general users, researchers, annotators, students, educators, databases, bio-informaticians +

19. Annotator needs
Currently we use RasMol and NdbView for quick visualization and checking
For annotation, the visualization software should be capable of:
Quick display (especially for large complexes)
Displaying secondary structure
Selecting atoms or residues for display or rendering
Showing symmetry related molecules
Coloring all or selected residues or chains
Computing distances
Displaying standard and unusual ligands

20. Educator needs
Visualization programs for educators and students should:
Be free
Be open source
Be capable of running on multiple platforms (without browser dependence)
Be portable
Be easy to install and use
Have user friendly interface
Common themes from a survey of ~25 educators from all over the world

21. Educator requests and visions
Visualization software for educators and students should:
Be more interactive so that students can for example, make mutations in the structure
Have better control on superposition of structures
Have an undo command
Be able to import and export more file formats
Have both a menu driven and command line interface
have different interfaces for research and education and perhaps have a tunable interface
Be a multifunctional suite of programs that can all read the same or related formats

22. Summary: how do we proceed from here?
How do we ensure that large biological molecules like viruses and ribosomes are uniformly represented in the PDB file?
How do we create a channel of communication between the user community and visualization software developers in order to develop better visualization resources?