Re: [Chimera-users] Just want atom distances

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 Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu 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) OCICB/OSMO/OD/NIAID/NIH

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) http://exon.niaid.nih.gov (Public)

Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

From: Eric Pettersen mailto:pett@cgl.ucsf.edu> To: "chimera-users@cgl.ucsf.edumailto:chimera-users@cgl.ucsf.edu BB" mailto:chimera-users@cgl.ucsf.edu> Cc: Patricia LiWang mailto:pliwang@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