Changing radius of individual atoms

General Discussion
1

Hello Avogadro,

I am brand new to this wonderful software.

Can one change the radius of individual atoms-- either within Avogadro, or after export using another software ?

Thank you !

Sunny

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2

Hi Sunny,

On Sun, Aug 12, 2012 at 9:28 AM, Dzik, Walter H.,M.D.
SDZIK@partners.org wrote:

Can one change the radius of individual atoms-- either within Avogadro, or after export using another software ?

Within avogadro, use the selection tool (F11) and right click on the
atom you want to modify. There should be a change radius option in the
menu that pops up.

Hope this helps,

Dave

3

Hello Mr Lonie,

Thank you so very much for writing back. Unfortunately, I don’t get that pop up. I am certain that I am inthe F11 selection tool. When I right click, I only see arrows in the horizontal and vertical direction which allow me to laterally move the entire molecule around on the background.

I am using the windows version…on Windows XP… the version is 1.0.3…downloaded just yesterday.

This is a marvelous software and so I hope to get the hang of it. I would love to do 2 things:

a) change the radius of individual atoms
b) be able to export a “movie file” (like an avi file) of the molecule while it is spinning using the “auto rotation tool”

If you can help with either of these two items, I would be quite grateful. I would like to publish an image using avogadro and cite it so that others will see it.

Best wishes,

Sunny Dzik
Mass General Hospital, Boston

From: David Lonie [david.lonie@kitware.com]
Sent: Sunday, August 12, 2012 11:48 AM
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] Changing radius of individual atoms

Hi Sunny,

On Sun, Aug 12, 2012 at 9:28 AM, Dzik, Walter H.,M.D.
SDZIK@partners.org wrote:

Can one change the radius of individual atoms-- either within Avogadro, or after export using another software ?

Within avogadro, use the selection tool (F11) and right click on the
atom you want to modify. There should be a change radius option in the
menu that pops up.

Hope this helps,

Dave

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4

Thank you so very much for writing back. Unfortunately, I don’t get that pop up. I am certain that I am inthe F11 selection tool. When I right click, I only see arrows in the horizontal and vertical direction which allow me to laterally move the entire molecule around on the background.

Dave forgot that he’s using the development version, v1.1.

a) change the radius of individual atoms

No problem. Please try the pre-release for Windows:
http://avogadro.openmolecules.net/pettt/Avogadro-1.1.0-pettt.zip

This should have the menu that Dave mentioned.

b) be able to export a “movie file” (like an avi file) of the molecule while it is spinning using the “auto rotation tool”

So my best suggestion at the moment, is to use a screen capture software, like Jing (Screen Capture Software | Snagit | TechSmith)

Hope that helps,
-Geoff

5

Dear Geoff,

This worked PERFECTLY !!! …Thank you very much !!

I have already shared the name of this lovely software with a Professor of Physics at Boston College who does primary theoretical work at the interface of chemistry and physics…and with a really super-smart high school student from an exclusive private school in Washington DC who can’t wait to show this to her teacher.

For my part, I hope to use this to display the interdependence of important clinical relationships in children with malaria ! (if one turns off H-bonds and turns off valence restrictions, then the software offers a really intuitive and easy way to show networks).

Thank you so much for your help !

Sunny
Boston

From: Geoff Hutchison [geoff.hutchison@gmail.com]
Sent: Sunday, August 12, 2012 4:57 PM
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] Changing radius of individual atoms

Thank you so very much for writing back. Unfortunately, I don’t get that pop up. I am certain that I am inthe F11 selection tool. When I right click, I only see arrows in the horizontal and vertical direction which allow me to laterally move the entire molecule around on the background.

Dave forgot that he’s using the development version, v1.1.

a) change the radius of individual atoms

No problem. Please try the pre-release for Windows:
http://avogadro.openmolecules.net/pettt/Avogadro-1.1.0-pettt.zip

This should have the menu that Dave mentioned.

b) be able to export a “movie file” (like an avi file) of the molecule while it is spinning using the “auto rotation tool”

So my best suggestion at the moment, is to use a screen capture software, like Jing (Screen Capture Software | Snagit | TechSmith)

Hope that helps,
-Geoff

Live Security Virtual Conference
Exclusive live event will cover all the ways today’s security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/

Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net

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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
MyComplianceReport.com: Compliance and Ethics Reporting . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

6

Dear Geoff,
Having had a quick play, the new release of Avogadro looks particularly exciting. I hope to introduce it to every student (and member of staff) here at the school of Pharmacy so they can more readily build, visualize and most importantly conformer search their molecule of interest.

Previous versions have been well received, especially by my five year old son!

I am sure that all us who use this software will join me in thanking you and the entire team for making a free resource available that has the ability to enthuse, educate and inspire. Please continue with this excellent open source project and I hope that it goes from strength to strength.

All the Best,
Fyaz

Dr. Fyaz M. D. Ismail, B.Sc.(Hons.), Ph.D., M.A.P.S.; member of the ACS.
Medicinal Chemistry Research Group,
School of Pharmacy & Biomolecular Sciences,
Liverpool John Moores,
Byrom Street
Liverpool
L3 3AF
United Kingdom
Web page: http://www.ljmu.ac.uk/PBS/115994.htm
Tel:+44 0151 231 2231; Fax: Tel:+44 0151 231 2170

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