Importing molecule by name

General Discussion
1

Hello,

For some reason the Import - Fetch by chemical name function in Avogadro is not working today. When I try I get en error message: Specified molecule could not be loaded: toluene.sdf

I takes a minute or two before this error message appears.

I tried importing from the protein data bank and got the same type of message.

Does anyone know what would cause this? Is it on my end, or is the problem with the server that Avogadro fetches the structures from?

Thanks

Steve

Dr. Steven P. Wathen
Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657
swathen@sienaheights.edu

2

On Thu, Nov 19, 2015 at 10:35 AM, Steven Wathen
SWATHEN@sienaheights.edu wrote:

Hello,

For some reason the Import - Fetch by chemical name function in Avogadro is not working today. When I try I get en error message: Specified molecule could not be loaded: toluene.sdf

I takes a minute or two before this error message appears.

What version of Avogadro are you using, what platform is this on?

I tried importing from the protein data bank and got the same type of message.

Does anyone know what would cause this? Is it on my end, or is the problem with the server that Avogadro fetches the structures from?

The upstream service looks like it is working, we should add some more
explicit messages to the code for when this fails as it can be a
little too mysterious. It could be your end if the service was blocked
for some reason.

Marcus

3

Dear Avogadro, whwn I want to measure the C-C-distances in alkanes, i get
1,07 Angstroms instead of 1,64. Is it possible to adjust The measuring tool
in working with Avogadro?

4

Hello,

Try optimizing the geometry before measuring the angle:

                      Extensions menu  - Optimize Geometry

Steve

Dr. Steven P. Wathen
Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657
swathen@sienaheights.edu

From: Hpborusso@aol.com [Hpborusso@aol.com]
Sent: Sunday, November 22, 2015 5:02 PM
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] importing molecule by name

Dear Avogadro, whwn I want to measure the C-C-distances in alkanes, i get 1,07 Angstroms instead of 1,64. Is it possible to adjust The measuring tool in working with Avogadro?