[Chimera-users] Just want atom distances

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Mon Apr 30 12:52:28 PDT 2012

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?


Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)

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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.

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

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 Pettersen

                        UCSF Computer Graphics Lab


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