Cut-n-paste in Avogadro running on Ubuntu

General Discussion
1

Hi!

Avogadro’s cut-n-paste doesn’t work for me running on Ubuntu. Yes, you
can copy a XYZ-file from a terminal window and paste it into Avogadro.
However, say, you select 3 atoms in Avogadro and copy-n-paste it in the
same Avogadro window, it keeps pasting what was orginally stored (from
the Terminal window). Otherwise it seems to work great.

I have been using Avogadro for years on Mac OS-X and the program is very unstable, that’s why I decided to give Ubuntu a go.

It would be great to hear from someone about this!

Fredrik

2

Hi,

On Sat, Jan 19, 2013 at 10:52 AM, fredrik haeffner
jfhaeffner@hotmail.com wrote:

Hi!

Avogadro’s cut-n-paste doesn’t work for me running on Ubuntu. Yes, you can
copy a XYZ-file from a terminal window and paste it into Avogadro. However,
say, you select 3 atoms in Avogadro and copy-n-paste it in the same Avogadro
window, it keeps pasting what was orginally stored (from the Terminal
window). Otherwise it seems to work great.

Could you let me know what version of Avogadro and Ubuntu this is on?
I don’t use Ubuntu myself, but there are a few people in the office
who do so I could likely take a look. It works fine here on Linux
using Avogadro’s master from today (Arch Linux 64 bit). That code has
not changed very much, but I know Ubuntu is probably still on Avogadro
1.0.3 or so.

I have been using Avogadro for years on Mac OS-X and the program is very
unstable, that’s why I decided to give Ubuntu a go.

It would be great to hear from someone about this!

We have tried to reduce crashes, and with Avogadro 2 rewrite that is
something I am focusing on - a stable and well tested core. Work is
progressing well there, but it is not ready to replace Avogadro 1 yet.
The copy/paste code has not changed much, and I use that functionality
quite regularly on Linux.

Marcus

3

On Sat, Jan 19, 2013 at 1:23 PM, Marcus D. Hanwell
marcus.hanwell@kitware.com wrote:

Hi,

On Sat, Jan 19, 2013 at 10:52 AM, fredrik haeffner
jfhaeffner@hotmail.com wrote:

Hi!

Avogadro’s cut-n-paste doesn’t work for me running on Ubuntu. Yes, you can
copy a XYZ-file from a terminal window and paste it into Avogadro. However,
say, you select 3 atoms in Avogadro and copy-n-paste it in the same Avogadro
window, it keeps pasting what was orginally stored (from the Terminal
window). Otherwise it seems to work great.

Could you let me know what version of Avogadro and Ubuntu this is on?
I don’t use Ubuntu myself, but there are a few people in the office
who do so I could likely take a look. It works fine here on Linux
using Avogadro’s master from today (Arch Linux 64 bit). That code has
not changed very much, but I know Ubuntu is probably still on Avogadro
1.0.3 or so.

I have been using Avogadro for years on Mac OS-X and the program is very
unstable, that’s why I decided to give Ubuntu a go.

It would be great to hear from someone about this!

We have tried to reduce crashes, and with Avogadro 2 rewrite that is
something I am focusing on - a stable and well tested core. Work is
progressing well there, but it is not ready to replace Avogadro 1 yet.
The copy/paste code has not changed much, and I use that functionality
quite regularly on Linux.

Another point I just remembered about Ubuntu - they tend to break the
Open Babel package up, I have looked at other people’s systems where
installing all of the Open Babel packages made several features work
(I think missing data files is one culprit). This may have improved,
if not we should try and get in touch with the Ubuntu developer to get
them to adjust the dependencies of the Avogadro package.

Marcus

4

Hi Marcus,
It’s:

Distributor ID: Ubuntu
Description: Ubuntu 12.10
Release: 12.10
Codename: quantal

and

Avogadro:

Application 1.03

If you open Avogadro and build a molecule, you can select all (or partially) atoms, copy-n-paste it. That works fine. It is when you copy coordinates from a terminal window into Avogadro that is the problem. It works fine to paste those coordinates into Avogadro. It’s now the problem comes around. Copying and pasting in Avogadro now only results in pasting the coordinates copied from the Terminal window that is stored in the buffer, clipboard… oo whatever it’s called. The list that stores the coordinates doesn’t get updated. It’s a problem that makes me not being able to use Avogadro under Ubuntu.

On mac I have had other problems. The program crashes every time I am trying to paste coordinates into Avogadro or paste them into, say, Emacs. I have tried to remove Avogadro from the Mac and re-installed it. but the problem persists on that machine. I used Avogadro for 1 1/2 year on it until this now happens. Is it a memory allocation problem of some sort?

I love Avogadro and use it every day. best program around. It’s just that it bugs and crashes…

regards,

Fredrik

Date: Sat, 19 Jan 2013 14:49:53 -0500
From: marcus.hanwell@kitware.com
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] cut-n-paste in Avogadro running on Ubuntu

On Sat, Jan 19, 2013 at 1:23 PM, Marcus D. Hanwell
marcus.hanwell@kitware.com wrote:

Hi,

On Sat, Jan 19, 2013 at 10:52 AM, fredrik haeffner
jfhaeffner@hotmail.com wrote:

Hi!

Avogadro’s cut-n-paste doesn’t work for me running on Ubuntu. Yes, you can
copy a XYZ-file from a terminal window and paste it into Avogadro. However,
say, you select 3 atoms in Avogadro and copy-n-paste it in the same Avogadro
window, it keeps pasting what was orginally stored (from the Terminal
window). Otherwise it seems to work great.

Could you let me know what version of Avogadro and Ubuntu this is on?
I don’t use Ubuntu myself, but there are a few people in the office
who do so I could likely take a look. It works fine here on Linux
using Avogadro’s master from today (Arch Linux 64 bit). That code has
not changed very much, but I know Ubuntu is probably still on Avogadro
1.0.3 or so.

I have been using Avogadro for years on Mac OS-X and the program is very
unstable, that’s why I decided to give Ubuntu a go.

It would be great to hear from someone about this!

We have tried to reduce crashes, and with Avogadro 2 rewrite that is
something I am focusing on - a stable and well tested core. Work is
progressing well there, but it is not ready to replace Avogadro 1 yet.
The copy/paste code has not changed much, and I use that functionality
quite regularly on Linux.

Another point I just remembered about Ubuntu - they tend to break the
Open Babel package up, I have looked at other people’s systems where
installing all of the Open Babel packages made several features work
(I think missing data files is one culprit). This may have improved,
if not we should try and get in touch with the Ubuntu developer to get
them to adjust the dependencies of the Avogadro package.

Marcus

Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
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5

If we don’t hear about crashes or bugs, we can’t fix them. I use it on my Mac (indeed, the Mac version is built on my desktop) and haven’t had crashes, except of course on experimental code. :slight_smile:

I just tried copy/paste from Avogadro 1.0.3 and 1.1.0 into Aquamacs, and it was fine. Does this only occur on one Mac? What version of Emacs are you using?

Hope that helps,
-Geoff

On mac I have had other problems. The program crashes every time I am trying to paste coordinates into Avogadro or paste them into, say, Emacs. I have tried to remove Avogadro from the Mac and re-installed it. but the problem persists on that machine. I used Avogadro for 1 1/2 year on it until this now happens. Is it a memory allocation problem of some sort?
…
I love Avogadro and use it every day. best program around. It’s just that it bugs and crashes…

6

On Sat, Jan 19, 2013 at 8:50 PM, fredrik haeffner
jfhaeffner@hotmail.com wrote:

Hi Marcus,
It’s:

Distributor ID: Ubuntu
Description: Ubuntu 12.10
Release: 12.10
Codename: quantal

and

Avogadro:

Application 1.03

If you open Avogadro and build a molecule, you can select all (or partially)
atoms, copy-n-paste it. That works fine. It is when you copy coordinates
from a terminal window into Avogadro that is the problem. It works fine to
paste those coordinates into Avogadro. It’s now the problem comes around.
Copying and pasting in Avogadro now only results in pasting the coordinates
copied from the Terminal window that is stored in the buffer, clipboard… oo
whatever it’s called. The list that stores the coordinates doesn’t get
updated. It’s a problem that makes me not being able to use Avogadro under
Ubuntu.

I am using a KDE desktop with Avogadro master, but what you described
works fine here. I will see if I can get on an Ubuntu machine next
week, what terminal/window manager (Unity perhaps?) I seem to be able
to switch back and forth, but I rarely copy xyz files from a console.

On mac I have had other problems. The program crashes every time I am trying
to paste coordinates into Avogadro or paste them into, say, Emacs. I have
tried to remove Avogadro from the Mac and re-installed it. but the problem
persists on that machine. I used Avogadro for 1 1/2 year on it until this
now happens. Is it a memory allocation problem of some sort?

I love Avogadro and use it every day. best program around. It’s just that it
bugs and crashes…

As Geoff has said, he uses it and builds it on his machine. I have a
Macbook Pro I do some testing on too, and use a little (although my
main desktop is Linux). We will look into better diagnostics we could
add to binaries as I have never observed this very crashy issue on Mac
and it would be great to see a backtrace to understand what might be
causing it.

Thanks for the feedback, I will see if I can spot the issue on Ubuntu.
We are committed to producing a more stable application, I think there
are some exciting developments on the horizon. In the meantime, I will
see if there are any crasher bugs in 1.1 that we can track down and
remedy.

Thanks,

Marcus

7

Hi All,

I’ve tried to reproduce this as I’m on Ubuntu 12.04.1 LTS.

I built avogadro using avogadro-squared and the system qt (i.e. installed
with apt-get install qt-sdk) and then just fired up the binary (I didn’t
set any BABEL_LIBDIR or BABEL_DATADIR environment variables as this didn’t
seem to be needed).

I can’t seem to reproduce that bug (i.e. I can paste coordinates from the
terminal into avogadro and it creates the molecules), however it keeps
crashing when I select and then try and copy at atom.

I’ve submitted a bug report here:

https://sourceforge.net/p/avogadro/bugs/660/

Let me know if there’s anything I can do to help.

Best wishes,

Jens

On 20 January 2013 19:55, Marcus D. Hanwell marcus.hanwell@kitware.comwrote:

On Sat, Jan 19, 2013 at 8:50 PM, fredrik haeffner
jfhaeffner@hotmail.com wrote:

Hi Marcus,
It’s:

Distributor ID: Ubuntu
Description: Ubuntu 12.10
Release: 12.10
Codename: quantal

and

Avogadro:

Application 1.03

If you open Avogadro and build a molecule, you can select all (or
partially)
atoms, copy-n-paste it. That works fine. It is when you copy coordinates
from a terminal window into Avogadro that is the problem. It works fine
to
paste those coordinates into Avogadro. It’s now the problem comes around.
Copying and pasting in Avogadro now only results in pasting the
coordinates
copied from the Terminal window that is stored in the buffer,
clipboard… oo
whatever it’s called. The list that stores the coordinates doesn’t get
updated. It’s a problem that makes me not being able to use Avogadro
under
Ubuntu.

I am using a KDE desktop with Avogadro master, but what you described
works fine here. I will see if I can get on an Ubuntu machine next
week, what terminal/window manager (Unity perhaps?) I seem to be able
to switch back and forth, but I rarely copy xyz files from a console.

On mac I have had other problems. The program crashes every time I am
trying
to paste coordinates into Avogadro or paste them into, say, Emacs. I have
tried to remove Avogadro from the Mac and re-installed it. but the
problem
persists on that machine. I used Avogadro for 1 1/2 year on it until this
now happens. Is it a memory allocation problem of some sort?

I love Avogadro and use it every day. best program around. It’s just
that it
bugs and crashes…

As Geoff has said, he uses it and builds it on his machine. I have a
Macbook Pro I do some testing on too, and use a little (although my
main desktop is Linux). We will look into better diagnostics we could
add to binaries as I have never observed this very crashy issue on Mac
and it would be great to see a backtrace to understand what might be
causing it.

Thanks for the feedback, I will see if I can spot the issue on Ubuntu.
We are committed to producing a more stable application, I think there
are some exciting developments on the horizon. In the meantime, I will
see if there are any crasher bugs in 1.1 that we can track down and
remedy.

Thanks,

Marcus

Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
MVPs and experts. ON SALE this month only – learn more at:
http://p.sf.net/sfu/learnmore_123012

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Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options

8

On Mon, Jan 21, 2013 at 2:04 PM, Jens Thomas
jensthomas@users.sourceforge.net wrote:

Hi All,

I’ve tried to reproduce this as I’m on Ubuntu 12.04.1 LTS.

I built avogadro using avogadro-squared and the system qt (i.e. installed
with apt-get install qt-sdk) and then just fired up the binary (I didn’t set
any BABEL_LIBDIR or BABEL_DATADIR environment variables as this didn’t seem
to be needed).

I can’t seem to reproduce that bug (i.e. I can paste coordinates from the
terminal into avogadro and it creates the molecules), however it keeps
crashing when I select and then try and copy at atom.

I’ve submitted a bug report here:

Avogadro / Old Bugs / #660 Crash when copying atoms on Ubuntu 12.04

Let me know if there’s anything I can do to help.

Thanks for the backtrace, I have not seen that crash but will see if I
can figure out why we might be hitting it. This is with the superbuild
Open Babel from what I can tell too, let me see if I can reproduce
this later, it would be odd if it were Ubuntu specific.

Thanks,

Marcus