Structure Window : File Commands

• Open
• Network Load
• Save
• Save As
• Export PNG
• Realign Structures
• Preferences
• Set Fonts
• Exit

Open

Open a structure file from the local disk. This can be an ASCII or binary ASN1 file, which must contain data of either the Ncbi-mime-asn1 or Cdd types (which will always be true of files downloaded from NCBI structure-based servers). If a there is already a structure being viewed, you will be prompted to save any changes before opening the new file.

Network Load

This is a shortcut to loading particular structures. Enter either a 4-letter PDB code or an MMDB integer ID. Cn3D will connect to NCBI's MMDB database via the internet and download that structure directly, which you can then manipulate as usual or save to a local file if desired.

Save

Save the current data to a file on the local disk, using the same filename and data type as was initially loaded. Cn3D will assume all editing changes are to be kept.

Save As

Similar to Save except a dialog will appear in which you can choose a diectory and file name and specify either ASCII or binary type files.

Export PNG

Save the image currently displayed in the structure window to a PNG-format file. First, you will be prompted for a file name and path. Then you will see a dialog that allows you to control the image export parameters, with these fields:

• File name: the current path to the file to be saved.
• Width and Height: the size (in pixels) of the image. The dimensions can be smaller or larger than the current window; this is useful for creating small thumbnails, or high resolution images for hardcopy output.
• Maintain Aspect: keep the same relative width/height as the current structure window. If unchecked, the view may not correspond exactly to what you see in the structure window.
• Interlaced: whether to create an interlaced PNG file. Interlacing is mainly for web images; it is unavailable for larger images.

Once you have set all the appropriate parameters, hit OK. You will see a small progress meter as the file is created; you'll have to wait until export is finished before continuing.

Realign Structures

Re-compute the structure alignment(s) between multiple structures. Each structure will be realigned with the first structure of the alignment, according to a rigid body fit using only the alpha carbon coordinates of residues in aligned blocks. The RMSD between the coordinate sets for each pair of structures will be printed in the message log. If there are aligned columns selected in the sequence window, then a dialog will appear asking whether to use only the selected residues for structure alignment.

Preferences

Brings up the Preferences dialog. These are program configuration options that persist from one session to another. There are three panels in this dialog:

Quality: controls the faceting resolution of various 3D objects. OpenGL (the 3D graphics system used by Cn3D) draws "smooth" objects like spheres out of many small triangles. These options control just how small the triangles are: more triangles means a smoother, more rounded appearance, but which takes longer to draw - making Cn3D respond more slowly. The Presets buttons are a convenience to adjust an overall rendering quality, from Low which draws quickly but looks jagged, to High which may draw slowly but will look much nicer, especially in a large window or an exported image file. You can also choose between Perspective and Orthographic projections.

Cache: controls the Biostruc caching system. This is an advanced option and by default will not affect most users. Certain NCBI data files may not actually contain structure information, but only alignments and annotations, etc.; Cn3D has to use a network connection to download structures from NCBI's MMDB server. These structures can be cached in order to avoid repeatedly transferring the same structures over a slow network connection. This panel allows you to set the location of the cache, and limit the amount of disk space it will use.

Advanced:

• The CDD Annotations checkbox controls whether CDD annotation information is read-only (the default) or editable. Un-check this option if you want to edit the annotation information stored in a local CDD file.
• Max structures: a limit of how many structures to load from a file with a multi-structured alignment.
• Footprint residues: In certain BLAST operations (like self-hits), the alignment is restricted to the currently aligned footprint, for avoiding ambiguity with repeated domains. The "excess" specified here allows the alignment to extend that many residues beyond the existing footprint.
• Eye separation: controls the stereo view, how great the depth of the perceived stereo appears.
• Proximal: whether to use proximal (cross-eyed) or distal (uncrossed) stereo.
• Browser Launch: (UNIX ONLY) tells Cn3D how to launch a web browser on your system. The default is netscape, for which the launch command is:

  ( netscape -raise -remote 'openURL(<URL>)' || netscape '<URL>' ) >/dev/null 2>&1 &

  This brings up the document in an existing netscape window; if you want to use a new window for each document, use the command:

  ( netscape -noraise -remote 'openURL(<URL>,new-window)' || netscape '<URL>' ) >/dev/null 2>&1 &

  These command strings should be all on one line. You can customize the command to launch any browser you wish. Each occurrence of the string <URL> will be replaced by the actual URL of the web page Cn3D is launching.

Set Fonts

Exit