[Chimera-users] Just want atom distances

Eric Pettersen pett at cgl.ucsf.edu
Mon Apr 30 19:05:51 PDT 2012

Hi Darrell,
	Good idea.  I've implemented a version of this by adding an entry to  
the popup menu you get when you control-double-click an atom.  The  
menu will have a "Show distances to nearby atoms" entry that shows all  
distances to non-bonded atoms within 4 angstroms (and hides distances  
you showed previously).  If you bring up the menu a second time on the  
same atom the entry will be "Hide...(etc)".  The feature will be in  
tonight's daily build.  The actual menu text isn't set in stone so it  
might change slightly in the next few days but it'll still be obvious  
which entry it is.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Apr 30, 2012, at 12:52 PM, Hurt, Darrell (NIH/NIAID) [E] wrote:

> Hi everyone,
> This brings up a feature that I've been missing in all visualizers  
> that I've tried. It exists (or at least used to) in "O". When you  
> click on and select an atom using a special mouse modifier, the  
> software would "reach out" and display all distances to other atoms  
> within a pre-specified radius. Sometimes it is hard to judge how far  
> away other atoms are from a selected atom. The times I use measuring  
> tools the most is when I'm trying to identify "nearby" atoms. While  
> it is true that we have the "Zone" selection and similar tools, I  
> think that it would be really nice to have a tool that "looks for"  
> close contacts and displays their distances using pseudobonds given  
> a simple click. The next click would either turn off the pseudobonds  
> or display those associated with the next selected atom.
> Can you see what I'm trying to describe? Is this already possible  
> using a macro of some kind?
> Thanks,
> Darrell
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Office  301-402-0095
> Mobile 301-758-3559
> http://bioinformatics.niaid.nih.gov (Within NIH)
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> From: Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>>
> To: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>  
> BB" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
> Cc: Patricia LiWang  
> <pliwang at ucmerced.edu<mailto:pliwang at ucmerced.edu>>
> Subject: Re: [Chimera-users] Just want atom distances
> On Apr 30, 2012, at 9:54 AM, Elaine Meng wrote:
> 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.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html>
> 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
> Patricia,
> I think the thing you're missing is that control-click will select  
> an atom but in order to select a second atom without de-selecting  
> the first you need to shift-control-click the second atom.
> --Eric
>                        Eric Pettersen
>                        UCSF Computer Graphics Lab
>                        http://www.cgl.ucsf.edu

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