[Chimera-users] vdw define

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 1 10:16:21 PDT 2008

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  

(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"

(b) Start "Attribute Calculator" (under Tools... Structure Analysis)  
and calculate attribute "radius2" for "atoms" with the Formula:   
  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.

(c) Note the attribute assignment file is a very simple text format,  
described here:

One of the example files linked to the bottom of that page actually  
assigns radii by element:

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)
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 C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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

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