Hi Marta, Atomic radii are used not only in display of "spheres" but also to calculate molecular surfaces and find clashes/contacts. There are several ways to save radii. If you already set the radii with vdwdefine: (a) you could save a session, which remembers the changed radii and can later be restored (b) you can write all the radius values into an attribute definition file. Later if you open the *same* PDB you can reassign those radii by reading in the attribute definition file with the "Define Attribute" tool. If you have a set of radii that you want to apply to several different structures, I recommend this approach instead: (c) create your own attribute definition file with the desired radii. The file could be used repeatedly to assign radii to different structures using "Define Attribute." More details on each approach: (a) See "File... Save Session As" and "File... Restore" or commands "save" and "open" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html (b) Start "Attribute Calculator" (under Tools... Structure Analysis) and calculate attribute "radius2" for "atoms" with the Formula: atom.radius and turn on the option to "Save calculation results to file". That is, you aren't really calculating anything, just saving an attribute that already exists. Remember the name/location of the file. Text- edit the file and change "radius2" in its first line to "radius". Then in some later use of Chimera, if you open the same PDB file as the same model, you can reassign those radii: start Define Attribute (under Tools... Structure Analysis), browse to and open that attribute assignment file. This can only be used on the same structure open as the same model as before because the attributes assignment is by atom name/residue number/model number. Again I think approach (c) would be much better if you plan to apply the same radii to different structures. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ calculator.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ defineattrib.html (c) Note the attribute assignment file is a very simple text format, described here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ defineattrib.html#attrfile One of the example files linked to the bottom of that page actually assigns radii by element: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ midasrad.txt Approach (c) is more general and could be used on multiple different structures because the atoms do not have to be specified by atom name/ residue number/model number. The example uses element symbols, but you could use atom type (as under Select... Chemistry... IDATM type) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html or just the atom name (e.g. @CA) not including model number or residue number. You would just use your favorite text editor to create the file. In approach (b), using Attribute Calculator (or Render by Attribute) to write the file, the specifiers always include the residue numbers. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 1, 2008, at 2:42 AM, Marta Rossini wrote:
Hi all, I know in Chimera the existence of the command vdwdefine to set your desider vdw radius for a selection. My question is: it is possible to save this changes in a file (i.e. obtain a new file in any format convertible to pdb with the modified values)? or it's only a matter of visualization? thanks