[Chimera-users] Just want atom distances

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 30 09:54:48 PDT 2012

Hi Patti,
If you click the Help button on the Distances dialog, the resulting page lists three different ways to add the distance measurement:

	• The Create button creates a distance monitor between two atoms that have been selected (exactly two atoms must be selected).
	• Picking one atom and Shift-double-picking the second atom (that is, doubleclicking it with the button assigned to picking) elicits a button marked Show Distance. Clicking it creates the distance monitor and leaves the atoms in a selected state. Clicking elsewhere removes the button without creating a distance monitor but leaves the atoms in a selected state.
	• The command distance can also be used.

I'll try to clarify:
Picking from the screen is one way to make a selection.  Selection can also be done with menu or command.

So, you could either select two atoms (using picking or menu or command) and then click the Create button, as in method 1 above, or use method 2 picking with doubleclicking the second atom as you pick it instead of using the Create button.  Or method 3, distance command, for example:

distance :234.g at o :295.g at o

The bottom example in the "distances" manual page is for two atoms -- the only difference between turning a distance on and off is whether you use "distance" or "~distance"

Finally, this tutorial includes examples of measuring distances.

Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 29, 2012, at 4:49 PM, Patricia LiWang wrote:

> Hello users group,
> 	I don't want anything complicated-- I just want to get some rough distances between atoms.  So I go to
> Tools
> Structure Analysis
> Distances
> A window comes up with an empty table.  (No instructions on how to pick atoms)
> A search of the Chimera documentation tells me I have to Control-leftclick to pick two atoms
> But no matter how often I click and click and click, it never gives me anything.  I can't get even one atom to show up in the panel, let alone two. The side chains are sitting right there, getting clicked away, with nothing happening in the table.
> I am reading so many similar documentation pages, and apparently there is a difference between "selecting" and "picking"
> So I figure I'll just use the command line.  But the instructions don't even bother to tell you how to use the command line to get the distance between two atoms.  There is documentation on how to get distances between something and a "plane".
> Why do they make this so hard?  Surely this is the main "simple" thing people want to do with this program.  
> Would someone please tell me how to Pick or Select or Whatever two amino acids (any atom in them would be fine) and get a distance?  
> Or better yet, please tell me the exact command line command I can use to get the distance between 
> Asparate 234 carboxyl oxygen and Aspartate 295 carboxyl oxygen, both from chain "G"?
> Thanks!
> Patti

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