Protein Structure

CML is particularly; useful in managing protein structures as there is a complex mixture of information in most 'flat' files such as those from the Protein Data Bank (PDB). These include administrivia, citations, annotation, sequence, crystallography and 'small molecules' as well as the 3-D coordinates of the protein itself. Unfortunately most of this information is very rarely used because there is no useful way of managing it. (How many molecular modelling packages manage citations satisfactorily?).

This example includes two protein structures from PDB, each with points of interest for the markup. Remember that JUMBO is not intended to be a full molecular viewing and manipulation program, so don't expect high quality rendering! Note that the CML parser will only fully parse strict PDB files (there are a large number of mutant 'PDB-like' files in which the only communality is that they contain 'ATOM' cards; JUMBO does what it can with these).

Insulin

The PDB file 1insmini.pdb is a cut-down version (only a monomer is selected). The TOC

• ID is extracted from the HEADER
• COMPND and SOURCE are preserved as discrete objects. Wherever possible CML encapsulates existing pseudo-objects in an XVAR, ARRAY or XLIST. It is often possible to type these as (say) FLOAT or DATE. The semantics are added through DICTNAME and CONVENTION records so that CML-compliant software can apply appropriate methods to the objects. Thus CONVENTION="PDB" refers users to the PDB user manual and DICTNAME indicates the precise keyword in there. We strongly recommend this approach for anyone using CML documents with objects outside the range of this documentation.
• The PDB uses REMARK for annotations and comments. This is presently formatted à la FORTRAN but would benefit immensely from additional markup (e.g. for residues, tables, etc.).
• The PDB also uses REMARK for citations, and this is a tedious parsing problem. The CML parser has done this, so that all citations are fully structured BIB objects. under BIBLIST
• The sequences under SEQRES have been transformed to SEQUENCE objects, and labelled with their chain IDs ("Chain A"). Compare the displays with the SwissProt entry (remember that that was the preproprotein and that the B chain comes before the A!).
• The HET object refers to a dictionary of molecules and until this is translated into CML , HET is retained as a simple text string
.
• The secondary structure features (HELIX, SHEEET, TURN) are captured as FEATURES. (Maybe they should go under an XLIST container?). They contain pointers to other objects and subobjects in the CML document and the addressing is being developed
• SSBOND is captured as a FEATURE (DISULFID) and can be used to subaddress the appropriate atoms and residues. (This and subsequent objects are displayed in a later figure)
• SITE is also captured as a FEATURE and can use ARRAYs of (sub)addresses to identify all the components
• CRYST incorporates the CRYST, SCALE and MTRIX records. CML uses ARRAY and/or XLIST to manage matrices

Here is an expanded version of the citations (BIBLIST)

CML allows MOLs to contain other MOLs which is valuable for macromolecular structures. In this case the two chains of the molecule are held separately and it's up to the application how they are treated (for this example JUMBO is displaying the chains in separate windows with different orientations and scales, but they could be combined and ganged together).

The resulting CML file is 1ins.cml. It's no larger than the original PDB file and reads in much quicker as it doesn't need parsing.

Flavodoxin

This is an example of a protein with a single chain, but a small molecule ligand. The (edited) PDB file is 4fxnmini.pdb and a typical screenshot is