Functionality

I mentioned somewhere functionality of Avogadro, that needs to be addressed (improved, increased). I found a decent example of a functional software, that caught my eye. I am not suggesting copy it but it might be useful to take a look at for new ideas

http://www.chemcraftprog.com/download.html

Jonas

On May 6, 2009, at 10:42 PM, Jonas Baltrusaitis wrote:

I mentioned somewhere functionality of Avogadro, that needs to be
addressed (improved, increased). I found a decent example of a
functional software, that caught my eye. I am not suggesting copy it
but it might be useful to take a look at for new ideas

Since not all of us have access to Windows boxes, perhaps you’d be
willing to go through ChemCraft and/or other programs and pull some
ideas which you think are good? For example, I’m curious about the
PHASE software you mentioned on the CCL list as well. I also heard
about “MAPS,” a commercial package with somewhat similar aims to
Avogadro.

What really helps is a brief summary of how new features should work
– a “project specification” if you will. It’s easier to go from a
detailed specification to code, then from a list of features.

Jonas, this would be incredibly useful.

Create a new page on the wiki – maybe call it “Inspiration” or ideas
from other packages? We actually have an incomplete list on the wiki:
http://avogadro.openmolecules.net/wiki/Developer:Links

-Geoff

On Thu, May 07, 2009 at 12:31:32PM -0400, Geoffrey Hutchison wrote:

On May 6, 2009, at 10:42 PM, Jonas Baltrusaitis wrote:

I mentioned somewhere functionality of Avogadro, that needs to be
addressed (improved, increased). I found a decent example of a
functional software, that caught my eye. I am not suggesting copy it
but it might be useful to take a look at for new ideas

Since not all of us have access to Windows boxes,

There’s a GNU/Linux binary as well.

perhaps you’d be willing to go through ChemCraft and/or other
programs and pull some ideas which you think are good? For example,
I’m curious about the PHASE software you mentioned on the CCL list as
well. I also heard about “MAPS,” a commercial package with somewhat
similar aims to Avogadro.

I had a look a it, and while I can see some of the features mentioned on
their website are nice (z-matrix editor, other sort-of advanced ways to
modify molecules, “publication-style” black/white rendering of the
molecule) I have to say the first impression I have is that the GUI is
butt-ugly.

Furthermore, apparently you cannot rotate the molecule with your mouse,
you need to push buttons.

In general, I think xmakemol (an xmol clone,
http://www.nongnu.org/xmakemol/) has quite a nice interface for
viewing/displaying/measuring/animating smallish molecules; however it
uses modifier keys and more than one mouse button as well. But this is
the app I usually use to explore QM results as far structure goes
(xmakemol only reads .xyz and .pdb files AFAIK).

Michael

On Thu, May 07, 2009 at 06:44:12PM +0200, Michael Banck wrote:

In general, I think xmakemol (an xmol clone,
http://www.nongnu.org/xmakemol/) has quite a nice interface for
viewing/displaying/measuring/animating smallish molecules;

Here’s a screenshot, the GUI (being Motif) is butt-ugly as well, of
course:

Michael

no prob, will do. I would be glad to do that, didn’t want to overwhelm anybody with details, tough

— On Thu, 5/7/09, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

From: Geoffrey Hutchison geoff.hutchison@gmail.com
Subject: Re: [Avogadro-devel] functionality
To: jasius_1@yahoo.com
Cc: avogadro-devel@lists.sourceforge.net
Date: Thursday, May 7, 2009, 9:31 AM
On May 6, 2009, at 10:42 PM, Jonas Baltrusaitis wrote:

I mentioned somewhere functionality of Avogadro, that
needs to be addressed (improved, increased). I found a
decent example of a functional software, that caught my eye.
I am not suggesting copy it but it might be useful to take a
look at for new ideas

Since not all of us have access to Windows boxes, perhaps
you’d be willing to go through ChemCraft and/or other
programs and pull some ideas which you think are good? For
example, I’m curious about the PHASE software you
mentioned on the CCL list as well. I also heard about
"MAPS," a commercial package with somewhat similar
aims to Avogadro.

What really helps is a brief summary of how new features
should work – a “project specification” if you
will. It’s easier to go from a detailed specification to
code, then from a list of features.

Jonas, this would be incredibly useful.

Create a new page on the wiki – maybe call it
"Inspiration" or ideas from other packages? We
actually have an incomplete list on the wiki:
http://avogadro.openmolecules.net/wiki/Developer:Links

-Geoff

On Thu, May 7, 2009 at 11:44 AM, Michael Banck mbanck@gmx.net wrote:

I have to say the first impression I have is that the GUI is
butt-ugly.

Not everything can be Qt :wink:

Furthermore, apparently you cannot rotate the molecule with your mouse,
you need to push buttons.

OTOH, I think it would be nice to be able to rotate the molecule via
keyboard in avogadro – sort of a default manipulation mode that can
be used while drawing etc. One of the most frustrating things in avo
(for me at least) is not be able to navigate while drawing. Switch
tools every few seconds gets old fast. I’ll put in a request for this
while I’m thinking about it…

Dave

David Lonie wrote:

On Thu, May 7, 2009 at 11:44 AM, Michael Banck mbanck@gmx.net wrote:

I have to say the first impression I have is that the GUI is
butt-ugly.

Not everything can be Qt :wink:

Doesn’t mean it has to be so ugly either :wink:

Furthermore, apparently you cannot rotate the molecule with your mouse,
you need to push buttons.

OTOH, I think it would be nice to be able to rotate the molecule via
keyboard in avogadro – sort of a default manipulation mode that can
be used while drawing etc. One of the most frustrating things in avo
(for me at least) is not be able to navigate while drawing. Switch
tools every few seconds gets old fast. I’ll put in a request for this
while I’m thinking about it…

You can already rotate, translate and zoom the molecule using the
keyboard. Touch those arrow keys! I think it should be active in most
tools as none of them claim the keyboard events apart from navigate. May
be it needs more documentation - but that is already there :wink:

Jonas Baltrusaitis wrote:

no prob, will do. I would be glad to do that, didn’t want to overwhelm anybody with details, tough

I think that a wiki page with these ideas and inspiration would be
ideal. Geoff is right, there are quite a few other tools we are aware
of. I had seen the posts about this software on CCL too. Collating ideas
on wiki pages in related groups would probably be the most useful
approach in my opinion. We can also discuss them on here and the wiki page.

I think we all value input like this, even if we do not have the time to
work on the features at the moment they are suggested. As the number of
contributors increase more people would also be available to work on
these ideas. Most of which can be done with plugins, and so remain
nicely self contained extensions.

Thanks,

Marcus

On Thu, May 07, 2009 at 06:44:12PM +0200, Michael Banck wrote:

Furthermore, apparently you cannot rotate the molecule with your mouse,
you need to push buttons.

I take that back, you can rotate it using the right mouse button;
shit/ctrl-right mouse button translates.

Michael

OTOH, I think it would be nice to be able to rotate the molecule via
keyboard in avogadro – sort of a default manipulation mode that can
be used while drawing etc.

This should already work. Try the arrow keys with and without modifier
keys.

-Geoff

David Lonie wrote:

On Thu, May 7, 2009 at 12:17 PM, Marcus D. Hanwell marcus@cryos.org wrote:

You can already rotate, translate and zoom the molecule using the
keyboard. Touch those arrow keys! I think it should be active in most
tools as none of them claim the keyboard events apart from navigate. May
be it needs more documentation - but that is already there :wink:

Oh – then I suppose I can go close that request… How about modifier
keys? It looks like pressing Alt while clicking in draw mode does
something, but I can’t figure out what.

We already use Ctrl and Shift modifier keys to allow laptop/one mouse
button users to access the other mouse button functions. The same
modifiers are used with the arrow keys. Alt seems to be used globally by
KDE to move a window. So I am not sure on the best approach here.

One possibility is an application setting - I have a three button mouse
and want the modifier keys to do other things. That might work. Would
that be intuitive? We also need to work hard on actually documenting
these features in an approachable fashion.

Hi,

For example in VMD you can use 3 different keys to enable different modes:
r-rotate
t-translate
s-scale

Marius

On Thu, May 7, 2009 at 7:28 PM, Marcus D. Hanwell marcus@cryos.org wrote:

David Lonie wrote:

On Thu, May 7, 2009 at 12:17 PM, Marcus D. Hanwell marcus@cryos.org
wrote:

You can already rotate, translate and zoom the molecule using the
keyboard. Touch those arrow keys! I think it should be active in most
tools as none of them claim the keyboard events apart from navigate. May
be it needs more documentation - but that is already there :wink:

Oh – then I suppose I can go close that request… How about modifier
keys? It looks like pressing Alt while clicking in draw mode does
something, but I can’t figure out what.

We already use Ctrl and Shift modifier keys to allow laptop/one mouse
button users to access the other mouse button functions. The same
modifiers are used with the arrow keys. Alt seems to be used globally by
KDE to move a window. So I am not sure on the best approach here.

One possibility is an application setting - I have a three button mouse
and want the modifier keys to do other things. That might work. Would
that be intuitive? We also need to work hard on actually documenting
these features in an approachable fashion.


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Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

I am not sure how that would differ from just requesting features. I usually do that with word document containing a detailed description. I am not good at creating and managing websites

you mentioned PHASE, you all have to see their GUI and it’s functionality. While it’s good for everything related only with PHASE, it would be outstanding to have some options integrated to process a broad range of packages via Avogadro. Data processing and plotting… Killer, you ought to see it. I will try to come up with a functionality description in data processing part and put it on the feature request. This goes to many packages as they randomly plot various data (spectra, DOS etc) in various formats. Would be nice to have all of those being able to display and do any related spectral processing in Avogadro. PHASE Linux GUI can be downloaded from the website, try it not as software developers but as users that need functionality. You’ll be shocked, those guys surely new what they were doing (…and don’t call me Shirley…)

http://www.ciss.iis.u-tokyo.ac.jp/rss21/en/result/download/index.php#download_4

Jonas

PS. I just made a joke…

— On Thu, 5/7/09, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

From: Geoffrey Hutchison geoff.hutchison@gmail.com
Subject: Re: [Avogadro-devel] functionality
To: jasius_1@yahoo.com
Cc: avogadro-devel@lists.sourceforge.net
Date: Thursday, May 7, 2009, 9:31 AM
On May 6, 2009, at 10:42 PM, Jonas Baltrusaitis wrote:

I mentioned somewhere functionality of Avogadro, that
needs to be addressed (improved, increased). I found a
decent example of a functional software, that caught my eye.
I am not suggesting copy it but it might be useful to take a
look at for new ideas

Since not all of us have access to Windows boxes, perhaps
you’d be willing to go through ChemCraft and/or other
programs and pull some ideas which you think are good? For
example, I’m curious about the PHASE software you
mentioned on the CCL list as well. I also heard about
"MAPS," a commercial package with somewhat similar
aims to Avogadro.

What really helps is a brief summary of how new features
should work – a “project specification” if you
will. It’s easier to go from a detailed specification to
code, then from a list of features.

Jonas, this would be incredibly useful.

Create a new page on the wiki – maybe call it
"Inspiration" or ideas from other packages? We
actually have an incomplete list on the wiki:
http://avogadro.openmolecules.net/wiki/Developer:Links

-Geoff

just do that so everyone (even me) can contribute to it. something simple: upload screenshot or a quick drawing with a forum type of comments below

— On Thu, 5/7/09, Marcus D. Hanwell marcus@cryos.org wrote:

From: Marcus D. Hanwell marcus@cryos.org
Subject: Re: [Avogadro-devel] functionality
To: jasius_1@yahoo.com
Cc: “Geoffrey Hutchison” geoff.hutchison@gmail.com, avogadro-devel@lists.sourceforge.net
Date: Thursday, May 7, 2009, 10:20 AM
Jonas Baltrusaitis wrote:

no prob, will do. I would be glad to do that,
didn’t want to overwhelm anybody with details, tough

I think that a wiki page with these ideas and inspiration
would be
ideal. Geoff is right, there are quite a few other tools we
are aware
of. I had seen the posts about this software on CCL too.
Collating ideas
on wiki pages in related groups would probably be the most
useful
approach in my opinion. We can also discuss them on here
and the wiki page.

I think we all value input like this, even if we do not
have the time to
work on the features at the moment they are suggested. As
the number of
contributors increase more people would also be available
to work on
these ideas. Most of which can be done with plugins, and so
remain
nicely self contained extensions.

Thanks,

Marcus

Am Mittwoch, den 06.05.2009, 19:42 -0700 schrieb Jonas Baltrusaitis:

I mentioned somewhere functionality of Avogadro, that needs to be addressed (improved, increased). I found a decent example of a functional software, that caught my eye. I am not suggesting copy it but it might be useful to take a look at for new ideas

http://www.chemcraftprog.com/download.html

W00p, that’d be nice to have.

Carsten

whenever this website is created could you notify me? I am not sure but I think I am not receiving majority of avogadro-devel messages

— On Thu, 5/7/09, Marcus D. Hanwell marcus@cryos.org wrote:

From: Marcus D. Hanwell marcus@cryos.org
Subject: Re: [Avogadro-devel] functionality
To: jasius_1@yahoo.com
Cc: “Geoffrey Hutchison” geoff.hutchison@gmail.com, avogadro-devel@lists.sourceforge.net
Date: Thursday, May 7, 2009, 10:20 AM
Jonas Baltrusaitis wrote:

no prob, will do. I would be glad to do that,
didn’t want to overwhelm anybody with details, tough

I think that a wiki page with these ideas and inspiration
would be
ideal. Geoff is right, there are quite a few other tools we
are aware
of. I had seen the posts about this software on CCL too.
Collating ideas
on wiki pages in related groups would probably be the most
useful
approach in my opinion. We can also discuss them on here
and the wiki page.

I think we all value input like this, even if we do not
have the time to
work on the features at the moment they are suggested. As
the number of
contributors increase more people would also be available
to work on
these ideas. Most of which can be done with plugins, and so
remain
nicely self contained extensions.

Thanks,

Marcus