Tips for Quanta

For questions regarding Quanta, please contact Peter Hwang. If you know of other tips for using Quanta, or would like to post questions regarding Quanta on this web page, please email me at cynthia@msg.ucsf.edu.

Program Description

Quanta can be used for model/map visualization, and for automatically and/or interactively building a model into electron density, searching for alternate conformations, adding waters, etc.

To Use Quanta...

  1. Add to your .cshrc file:

      source ~msi/quanta98/.setquanta

  2. To start the program, type "quanta".

NOTE: There are currently (4/25/00) a limited number of licenses for Quanta. Please save changes and quit from Quanta if you expect to break from working for a period of time! Thanks!

Manual

A tutorial guide to key modules, including X-POWERFIT, X-BUILD, and X-SOLVATE can be found in /public/apps/msi/quanta98/tutorial. I have included links to particular sites in this tutorial below. However, I strongly recommend running through the tutorial to learn Quanta--don't rely on the notes below!

Getting Started--A Beginner's Guide to Quanta

 

To get started, look at the "Getting Started--First Tutorial" link in the tutorials (start.html). This explains how to review the rest of the tutorial. It's a pretty good page that goes over the skills that you are likely to need for refining. (Provided by Sandra Waugh, user of Quanta.)

  • Moving the Molecule: The tutorial describes how to rotate/translate the molecule using the virtual dial box, mouse ("virtual track ball"), and in X-AUTOFIT:X-BUILD: see the Move Tutorial. In general, rotate the molecule holding down MIDDLE mouse button; to zoom and translate, hold down the SHIFT key.
  • Identifying atoms: Click on the atom with the left mouse button... this will give the resid and atom type.
  • Pointer (setting display center): Quanta uses the Pointer to identify an atom as the active atom, and to consequently center the display on that atom. Access the pointer menu from the X-AUTOFIT:X-BUILD palette.
  • Loading in a PDB: From the main Quanta window... File --> Import. Quanta stores the PDB (and last display position on screen) as a ".MSF" file (open a particular MSF file using... File --> Open).
  • Loading in a Map: First, make sure that you have exited any applications (X-POWERFIT, X-BUILD, etc.). From the main Quanta window... Draw --> Map Table --> Show Map Table; in the Map Table... Maps --> Import. I've had success opening maps in CCP4 format. Use 6d_mapman to convert a CNS-generated map into CCP4 format (read in the map, then normalise, then write to CCP4 format). It may take 5 min or more to load in the map. When it is ready, a contour window will appear. To indicate contour levels in units of sigma, click first on "sigma level", then indicate the sigma level for the map (the map will be drawn at this contour level if "include" is marked). The map(s) won't appear until an Application is started. In the map table, click on the purple contour level to toggle its display on and off.
  • Log file: To save a log of the comments in the Quanta Textport, from the main Quanta window... File --> Log Output.
  • Command log file: To save a log of the commands you will be using during the session, from the main Quanta window... File --> Record Session.
  • Saving PDB file: To save your changed model in PDB format, from the main Quanta window... File --> Export.

 

Tips from Quanta Users

  1. X-SOLVATE--Save your work!! When leaving an application (ex, X-SOLVATE), make sure you "EXIT" if you want any changes made to the model to be saved; "QUIT" will result in loss of these changes (Quanta does NOT warn you of this!) (Provided by Cynthia Fuhrmann)
  2. Making Maps: The tutorial tells you how to import a map through the map table, but you may have to do some editing first. Quanta will only take XPLOR-ASCII maps if they have 9 or fewer remark lines at the top. You may need to delete a few lines to get it to load. If you don't delete these lines, the maps will still be drawn, but none of the real space refinement will work. (Provided by Sandra Waugh) (This does not seem to be a problem for CCP4-format maps.)

Site last updated 4/25/00 by Cynthia Fuhrmann.