For structure records, URLs should be of the form:
to retrieve the Structure Summary page. The UID portion of the URL should be the accession number only (uid=1OMD rather than uid=pdb|1OMD| ).
For structure records, it is possible for your link to directly launch Cn3D by setting dopt=i. However, the preferred entry point for structure records is the structure summary page (dopt=s), rather than the 3-D image itself, because it provides image viewing controls, as well as flat images for some of the structures. If you launch Cn3D directly, you cannot access those options.
If you still prefer to launch Cn3D directly, you can use the URL format below. It will give the default NCBI all-atom model for the PDB file "1OMD"
The URL below will load the Virtual Bond Model -alpha carbons, phosphates, and all heterogens.
Other options are...
It is also possible to link to structures (as well as sequences and MEDLINE records) using the instructions in the help documents on Creating Links to Web Pages in the Entrez System, Linking to Records in the Entrez System, and Creating a Web Link to PubMed. .