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3D atom Collection

 
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grumpy_labrat



Joined: 03 Aug 2008
Posts: 170
Location: University of Oregon

PostPosted: Fri Sep 10, 2010 4:37 pm    Post subject: 3D atom Collection Reply with quote

I'm curious about this 3D atom collection module in DT, but I can't find any information about what type of file it takes. Does someone use this module and would they be willing to comment?
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David
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Joined: 25 Nov 2006
Posts: 1964
Location: Chapel Hill, NC

PostPosted: Sat Sep 11, 2010 12:26 pm    Post subject: Reply with quote

This is pretty old and created for Gaussian output files. It has not been updated for a long time. A previous version of DT (on OS 7/Cool supported protein structures but that did not get re-implemented when I rewrote the app for Rhapsody in '97.

David
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grumpy_labrat



Joined: 03 Aug 2008
Posts: 170
Location: University of Oregon

PostPosted: Sat Sep 11, 2010 8:01 pm    Post subject: Reply with quote

Any chance that you could tie that module into OpenBabel?
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David
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Joined: 25 Nov 2006
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PostPosted: Sat Sep 11, 2010 8:22 pm    Post subject: Reply with quote

I could make this easier. Currently the "From File" module allows you to write a shell script that should be run before parsing the file (as an xyz) file.

I looked at the OpenBabel site and I will think about making it easy to call OpenBabel from within DataTank. Certainly it is no problem for me to launch it as a shell script.

David
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grumpy_labrat



Joined: 03 Aug 2008
Posts: 170
Location: University of Oregon

PostPosted: Sat Sep 11, 2010 8:28 pm    Post subject: Reply with quote

It would definitely be handy to be able to convert the various files into something DT handles already. I use a lot the .cif files, and it would be nice to be able to open them in DT.
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ghutchis



Joined: 12 Dec 2009
Posts: 20
Location: Pittsburgh, PA

PostPosted: Sun Sep 12, 2010 12:32 pm    Post subject: Reply with quote

uolabrat wrote:
It would definitely be handy to be able to convert the various files into something DT handles already. I use a lot the .cif files, and it would be nice to be able to open them in DT.


David brought this thread to my attention. (I'm one of the Open Babel developers.) I'm more of a DG user than a DT user, so I can't give you an immediate answer.

Babel already reads CIF, so it shouldn't be a problem. If you're willing to use the command-line, try:

babel [path-to-file.cif] -oxyz [path-to-new-file]

Now, this depends a bit on your CIF -- it will only output the unique atoms, not generate the full unit cell. Does that work for you?
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grumpy_labrat



Joined: 03 Aug 2008
Posts: 170
Location: University of Oregon

PostPosted: Sun Sep 12, 2010 4:45 pm    Post subject: Reply with quote

The idea would be to use it to create some nice figures with the fully populated unit cell, and to explore some of the other data that chemists run into: electron density, etc. iBabel makes it pretty easy to do the conversion, but I'm all about simplifying my work flow. So when I'm working in DT, I kind of want to do everything in DT. I guess that I could use something else like crystalmaker or vesta to populate a full unit cell and export it into an .xtal format, which I could then export into a gaussian format for the module.
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grumpy_labrat



Joined: 03 Aug 2008
Posts: 170
Location: University of Oregon

PostPosted: Mon Sep 20, 2010 4:00 pm    Post subject: Reply with quote

Let me first retract that previous feature request. I just discovered that the atom collection will support the xyz format which is more than sufficient for what I'm after... not reading the documentation strikes again!... But I can't seem to be able to color the atom collection... is there a way to do that?
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David
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Joined: 25 Nov 2006
Posts: 1964
Location: Chapel Hill, NC

PostPosted: Tue Sep 21, 2010 9:59 pm    Post subject: Reply with quote

What do you mean by color? You can drag the atom collection into a drawing context and I use predefined colors for each atom type. Are the colors not set or not what you expect?

You can extract the position of the atoms as a 3D Point Collection and then draw that collection any way you want.

David
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