• Is there a replacement for Cn3D?


• Can Cn3D print?


• My Internet connection is slow...


• Why doesn't Cn3D read in PDB files?


• How do I link to MMDB/Cn3D?


• Can I get a local copy of the entire MMDB database?


• Is the source code for Cn3D available?


• Does Cn3D have a command-line interface?


• Why is no color change observed after switching to Color | Neighbor in some cases?


• Can I structurally align proteins in Cn3D or do I have to use the VAST web page?

Yes, the web-based viewer iCn3D has been developed as a replacement, does not require local installation (it runs in your web browser), and has most of the features introduced with Cn3D, plus many more!

No, not directly. But you can create a PNG image (File:Export PNG), and then use your favorite image processing software to print it out.

Instead of doing a network retrieval for every time you want to look at the same structure, you can save a structure to your computer using "File | Save" , the re-load it into the Cn3D window from the "File | Open | File" menu.

Cn3D reads only data files from the MMDB database, not PDB formatted records. MMDB is derived from the PDB database, but is corrected for naming-problems, performs domain-splitting, assigns consistent secondary structures, adds complete bonding information, and finally makes protein sequences corresponding exactly to the residues that appear in the structure. This work is done by a series of programs not possible to include in Cn3D. (The MMDB help document provides more information about the how the PDB data are processed and some examples of differences between MMDB and PDB records.)

For structure records, URLs should be of the form:

.../Structure/mmdb/mmdbsrv.cgi?db=t&form=6&uid=1OMD&dopt=s

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"

.../Structure/mmdb/mmdbsrv.cgi?db=t&form=6&uid=1OMD&Dopt=i

The URL below will load the Virtual Bond Model -alpha carbons, phosphates, and all heterogens.

.../Structure/mmdb/mmdbsrv.cgi?db=t&form=6&uid=3CRO&Dopt=i&Complexity=Virtual+Bond+Model

Other options are...
&Complexity=Virtual+Bond+Model
&Complexity=All+Models
&Complexity=Up+to+5+Models

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. .

No, the FTP distribution of MMMDB data has been discontinued

Yes. Cn3D is part of the NCBI C++ Toolkit (although it also requires wxWidgets). Cn3D has been designed with an open implementation, and is suitable for further development for special-purposes.

Because there is no commonly aligned regions among all the currently selected(displayed) structures. Try turning off some non-master structures using the "Alignment>Show/Hide Rows" menu item in the sequence alignment viewer.

It's easiest to use the VAST database of precomputed structure and sequence alignments.

You can also import structures from MMDB, but you have to manually create a corresponding sequence alignment before you can align the structures.

If you have a structure that is not in our structure database, you can use the vast search service to find alignments to structures in our database, and then view the superpositions in Cn3D.