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Kalzium @ 3D, Part III

Taken in Portugal
Benoit and myself improved the 3D-feature again. For all "chemistry" we are using OpenBabel. Well, we quickly learned that OpenBabel2.0 didn't provide everything what we needed. So in true OpenSource-spirit we simply hacked OpenBabel ;-) Well, as a result OpenBabel now supports an better way to calculate the angles between three atoms, has a more precise and less error-prone math-code for doings specific calculations and can calculate the volume of so called Unit Cells.
With all that done, Kalzium now requires OpenBabel 2.1-preview as of yesterday ;-) But As OpenBabel 2.1 will be released in two or three month that shouldn't be a problem, the 3D-feature is not compiled of OpenBabel 2.1 is not found anyway.

Ok, this is the result of our hacking:

Free Image Hosting at www.ImageShack.us

As you can see the molecule is on the right, you can simply rotate it with your mouse. On the left you have an overview over all atoms in the molecule. If you select an atom there it will be highlighted in the 3D-view (see the blue blur around two atoms?). The number in the QTreeWidget is the internal ID of the atom. I am not sure what information to put into that treewidget. If you have ideas please comment to this blog or write a mail to kalzium AT kde DOT org. That is of valid for the whole GUI. Any idea might lead to a better GUI!
Currently the widget supports for different "designs" of the rendered molecule. I GIMP'ed a little to show you all in one view:

Free Image Hosting at www.ImageShack.us

The molecule you see is 7H-Purin-6-amine and includes some double bonds. Again: Do you see room for improvements? If so, tell us :-)

PS: The rendering was done without hardware acceleration but is very fast
PPS: This is the lowest of three quality levels. The best looks much better but I forgot to switch to it when doing the screenies

Comments

( 101 comments — Leave a comment )
Page 1 of 2
<<[1] [2] >>
(Anonymous)
Jul. 22nd, 2006 02:38 pm (UTC)
2D-View
This all looks very nice but also useful would be a 2D-view of the molecules. I'm thinking of a possibility to export the 2D-view as a png, svg, or whatever to use it in latex or kword.
cniehaus
Jul. 22nd, 2006 03:17 pm (UTC)
Re: 2D-View
Well, Openbabel understands also 2d files but this widget is of course made for 3d. If you have the 2d-information you don't need to use Kalzium to export as PNG as for that task you should use a Moleculeeditor I think...
(Anonymous)
Jul. 23rd, 2006 01:57 am (UTC)
names of atoms
hi
well I had a look at it and it is really awesome. I had some problems guessing which atom is which, maybe you can make it, so that te names or abbriviations are displayed on the atom. like a H rendered on the hydrogen atom or something like that.

~matti~
(Anonymous)
Jul. 23rd, 2006 08:24 am (UTC)
Re: names of atoms
Yes, we are planning to do that. We'll also provide the ability to display other information on the molecule, like the angles between bonds etc.

-Benoit
(no subject) - sandytifev - Jul. 16th, 2008 01:11 am (UTC) - Expand
(no subject) - daronsalmond - Aug. 6th, 2008 03:52 am (UTC) - Expand
(no subject) - cedricmarcil - Aug. 10th, 2008 10:27 pm (UTC) - Expand
(no subject) - bufordmayberry - Aug. 11th, 2008 01:47 am (UTC) - Expand
(Anonymous)
Jul. 23rd, 2006 06:40 am (UTC)
Names of Atoms and Functional Groups
I just read this blog and i gotta say good job.

As for improvements, I would try to implement something that draws the abbreviations of the atoms on the 3d-atom itself.

I also figured, that it would be nice, if a 'sphere' or something was drawed around functional groups and it would display the name of the functional group on it.

Like if u had a C3H7COOH atom, a sphere was drawed around the COOH and it would display COOH on it.
cniehaus
Jul. 23rd, 2006 08:41 am (UTC)
Re: Names of Atoms and Functional Groups
This is our todo

* 3D-Viewer
- implement ghemical-like zoom/navigation
- Crystal Viewer
-- For lattice
-- All Brevies cells
-- User defined distances (length of the vectors)
-- User defined angles (alpha, beta, gamma)
-- Show oktaedral and tetragonal void. For an oktaedral void:
http://upload.wikimedia.org/wikipedia/de/6/61/Kfz_oktaederluecke.png
- Molecule Viewer
-- Export as graphic (PNG, JPEG...)
-- Autorotation
--- The user should be able to define which axes are
rotated and in which speed
--- This could even be exported into a .gif-file or something
as an animation
-- If the user selects an atom in the GL-view highlight
that atom and also in the QTreeWidget
-- Calculations
--- the distance between two atoms
--- the angle and/or the torsion between three atoms
-- Drawing symbols into the position of an atom.
For reference: http://smid.blueprint.org/images/107/pc442107.png
-- Drawing a plane through 3 atoms. Look
http://www.crystal.unito.it/tutojan2004/tutorials/I_surface/image006.gif
http://en.wikipedia.org/wiki/Bragg_diffraction
-- Making the 3D-Viewer a standalone app or a KPart
--- If the user clicks on a cml-file for example then the app opens and
renders the content in 3D.
--- Kalzium would just use this app/KPart
-- Zooming in and out
Re: Names of Atoms and Functional Groups - (Anonymous) - Jul. 24th, 2006 12:59 pm (UTC) - Expand
Re: Names of Atoms and Functional Groups - cniehaus - Jul. 24th, 2006 01:43 pm (UTC) - Expand
Re: Names of Atoms and Functional Groups - (Anonymous) - Jul. 24th, 2006 02:14 pm (UTC) - Expand
Re: Names of Atoms and Functional Groups - cniehaus - Jul. 24th, 2006 02:23 pm (UTC) - Expand
Re: Names of Atoms and Functional Groups - (Anonymous) - Jul. 24th, 2006 05:46 pm (UTC) - Expand
(no subject) - monikageer - Aug. 6th, 2008 03:59 am (UTC) - Expand
(no subject) - esterwoodhall - Aug. 11th, 2008 09:04 am (UTC) - Expand
(no subject) - mauroramer - Aug. 11th, 2008 12:11 pm (UTC) - Expand
(Anonymous)
Jul. 24th, 2006 10:08 am (UTC)
TreeView
Just a simple idea: Show the name of the Atom in the TreeView.
Is there also an entry for the bindings in the TreeView? -> If so, show the kind of binding (single, double,...)
cniehaus
Jul. 24th, 2006 10:28 am (UTC)
Re: TreeView
* Huh? The names are in the treeview (they are grouped in "Carbon" and so on)

* Well, a carbon-atom for example can have for example a tripple and a single bond, or 4 singles, or 2 double, or only one double... Very hard to sort that kind of thing...
(no subject) - rickietogni - Aug. 6th, 2008 04:33 am (UTC) - Expand
(no subject) - tylersantisteb - Aug. 10th, 2008 11:55 pm (UTC) - Expand
(no subject) - bryonfinacy - Aug. 11th, 2008 02:46 am (UTC) - Expand
(no subject) - cristobalpoore - Aug. 11th, 2008 05:28 am (UTC) - Expand
(no subject) - maynardlongori - Aug. 11th, 2008 06:45 am (UTC) - Expand
(no subject) - danterobe - Aug. 12th, 2008 12:07 pm (UTC) - Expand
(Anonymous)
Jul. 24th, 2006 12:48 pm (UTC)
Questionable source of coordinates
Hi,
I was just looking at your picture of "7H-Purin-6-amine" and I found *several* mistakes:
a) two double bonds are missing, between 4-5 and 1-6
b) the nitrogen at 7 looks as if it was sp3-hybridized, but in fact the hydrogen atom should be coplanar with the whole ring system
c) the amino group is that of an aliphatic amine. In aromatic systems the lone pair of the nitrogen is usually delocalized into the ring system. As a consequence the amino group is planar and both hydrogen atoms are coplanar with the ring system.

Altogether, the source of the structure appears to be very questionable. I hope that Kalzium will only ship with reliable structures, i.e. X-Ray geometries (CSD) or NMR structures from the Protein Data Bank (http://www.pdb.org/).
BTW, I would also like to see that the molecule is commonly called "adenine" ;-)
And finally thanks for all your efforts and work to bring KDE closer to chemistry!
(Anonymous)
Jul. 24th, 2006 01:05 pm (UTC)
Re: Questionable source of coordinates
Just to answer a) : depending on the viewing angle, some double bonds can look like single bonds. You can just rotate around to see the double bonds properly.

I can't answer the rest as I'm no chemist, but surely Carsten can

-Benoit
Re: Questionable source of coordinates - (Anonymous) - Jul. 24th, 2006 01:11 pm (UTC) - Expand
Re: Questionable source of coordinates - cniehaus - Jul. 24th, 2006 01:17 pm (UTC) - Expand
Re: Questionable source of coordinates - (Anonymous) - Jul. 24th, 2006 01:35 pm (UTC) - Expand
Re: Questionable source of coordinates - cniehaus - Jul. 24th, 2006 01:40 pm (UTC) - Expand
Re: Questionable source of coordinates - cniehaus - Jul. 24th, 2006 01:41 pm (UTC) - Expand
Re: Questionable source of coordinates - (Anonymous) - Jul. 24th, 2006 02:19 pm (UTC) - Expand
Re: Questionable source of coordinates - cniehaus - Jul. 24th, 2006 01:13 pm (UTC) - Expand
Re: Questionable source of coordinates - (Anonymous) - Jul. 24th, 2006 01:28 pm (UTC) - Expand
Re: Questionable source of coordinates - cniehaus - Jul. 24th, 2006 01:37 pm (UTC) - Expand
Re: Questionable source of coordinates - (Anonymous) - Jul. 24th, 2006 02:25 pm (UTC) - Expand
Re: Questionable source of coordinates - cniehaus - Jul. 24th, 2006 02:28 pm (UTC) - Expand
Re: Questionable source of coordinates - (Anonymous) - Jul. 24th, 2006 05:51 pm (UTC) - Expand
(no subject) - noreenewyji - Jul. 11th, 2008 12:34 am (UTC) - Expand
(no subject) - bryonweyer - Aug. 11th, 2008 04:28 am (UTC) - Expand
(no subject) - rachellesundhe - Aug. 11th, 2008 11:43 am (UTC) - Expand
(Anonymous)
Jul. 24th, 2006 01:06 pm (UTC)
Audience of Kalzium 3D?
Just a simple question:
For what kind of users do you develop Kalzium 3D?
Is it still an "educational" software for teaching pupils?
Or do you have scientists in mind?
cniehaus
Jul. 24th, 2006 01:15 pm (UTC)
Re: Audience of Kalzium 3D?
I am a chemistryteacher and plan to use Kalzium next year (after the summer holidays) in my own classes. For that some features are still missing but we are catching up.

As for scientists: They usually use very specialiced tools. And there are very advanced tools like PyMOL. But they mostly have such a **** userinterface that I can easily imagine that a Prof will use Kalzium in his lessons to demonstrate things. Why not?
(Anonymous)
Jul. 25th, 2006 09:18 am (UTC)
wikipedia integration
great job!
one question: are you thinking about integrating wikipedia into kalzium?
cniehaus
Jul. 25th, 2006 09:32 am (UTC)
Re: wikipedia integration
Yes :) But that will happen later this year, perhaps in November or so.
(no subject) - elvingoold - Aug. 11th, 2008 01:29 am (UTC) - Expand
(no subject) - estebanmooradi - Aug. 11th, 2008 02:24 am (UTC) - Expand
(no subject) - katehienonen - Aug. 11th, 2008 03:58 am (UTC) - Expand
(no subject) - kurtisfoxtown - Aug. 11th, 2008 06:55 am (UTC) - Expand
skierpage
Jul. 25th, 2006 11:36 pm (UTC)
Kalzium not mentioned in OpenBabel wiki
Very nice stuff. The OpenBabel wiki's FAQ and Related_Projects pages don't mention Kalzium, they eventually should.
(Anonymous)
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(Anonymous)
May. 13th, 2007 11:41 am (UTC)
Re: Let's speak about the most important
I wonder if it is possible to marry different OSS projects and have one solid program. Why to reinvent everything?
http://jmol.sourceforge.net/screenshots/
Re: Let's speak about the most important - cniehaus - May. 13th, 2007 11:51 am (UTC) - Expand
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