Molecular Modeling Database banner graphic
NCBI Home PageNCBI Site Search pageNCBI Guide that lists and describes the NCBI resources
Structure Home 3D Macromolecular Structures Conserved Domains   PubChem    BioSystems 
 
 
 Cn3D macromolecular structure viewer
 
 
Frequently Asked Questions
 
   
 
back to top The Windows version of Cn3D crashes on startup or PNG export - how do I fix it?
 
 

Some OpenGL video drivers don't work with some of the rendering techniques used by Cn3D. There are two related things you can try to work around this:

  1. Disable some or all Windows graphics optimizations. Right-click on the desktop, select Properties, then the Settings tab, then hit Advanced, go to the Troubleshooting tab, and finally move the Hardware Acceleration one notch to the left. Hit Apply, Ok, Ok, to close the dialogs. Try Cn3D again; if the crash still occurs, repeat this procedure.


  2. If all that fails, try turning off OpenGL acceleration and optimization in your video card's graphics driver. Consult your documentation or system administrator for details. You may also want to install the latest graphics driver for your card.
 
 
back to top Can Cn3D print?
 
 

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.

 
 
back to top My Internet connection is slow...
 
 

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.

 
 
back to top On Windows, Cn3D shows a white screen...
 
 

The first thing to try is to turn off the Office toolbar if you are using it. If this does not work and your display card is an ATI Rage Pro (right click on the desktop, select properties, then select Settings to check), try reinstalling the driver.

 
 
back to top On Unix, Cn3D launches but doesn't show a structure.
 
 

Edit (or create) the .mailcap file in your home directory. Call up the file in any text editor and add the following line(s) if they don't exist already:

chemical/ncbi-asn1-binary; Cn3D %s
Make sure include the %s. See also the general instructions for configuring your browser.

 
 
back to top Why doesn't Cn3D read in PDB files?
 
 

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.)

 
 
back to top How do I link to MMDB/Cn3D?
 
 

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. .

 
 
back to top Can I get a local copy of the entire MMDB database?
 
 

Yes. Visit the MMDB FTP (ftp://ftp.ncbi.nih.gov/mmdb/) site.

 
 
back to top Is the source code for Cn3D available?
 
 

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.

 
 
back to top Does Cn3D have a command-line interface?
 
  No.

 
 
back to top Does Cn3D read RasMol scripts?
 
  No.

 
 
back to top Why does the screen flash colors when I move my mouse pointer out of the Cn3D window?
 
 

On computers that can only display 256 colors, Cn3D uses most of the color palette, which it time shares with other programs that are running. If you are running a web browser, try quitting out of the web browser.

 
 
back to top When first running Cn3D, why do I get an out of memory error?
 
 

If you are using a Macintosh, please try increasing the amount of memory available for the application. Increase the amount of memory in "Get Info" from the Finder to do this.

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

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

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

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.

 
 
 
 
 | Revised 26 September 2013 | | Help Desk | Disclaimer | Privacy statement | Accessibility |