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General Forums => Generic Discussion => Topic started by: AntiHeadshot on December 12, 2012, 11:36:00 AM

Title: Turn 2D structure into 3D (Leucine, Pyrrolysine, Valine, Glutamic Acid)
Post by: AntiHeadshot on December 12, 2012, 11:36:00 AM
(https://www.chemicalforums.com/proxy.php?request=http%3A%2F%2Fwww.molecularshirts.com%2Fimages%2Fpagemaster%2Flove_up_w_500.jpg&hash=5bc87b4f1f39c3083a368b66e6549d36)

My girlfriend loves chemistry, but i'm only a IT nerd, so i have no clue!  :-[

So I want to ask if someone can turn this 2D structure into a 3D, so I could build a model of it?
Title: Re: Turn 2D structure into 3D (Leucine, Pyrrolysine, Valine, Glutamic Acid)
Post by: Arkcon on December 12, 2012, 11:51:57 AM
Maybe its most visible, and cutest, just the way it is, with the elements identified by letters.  However, most university bookstores have molecular modeling kits, so yo can assemble them.  Once you do that, you'll have a better idea of how the atoms orient in 3-d space.  You might try to find a molecular modeling program, which will also draw ball and stick or space-filling models for you.
Title: Re: Turn 2D structure into 3D (Leucine, Pyrrolysine, Valine, Glutamic Acid)
Post by: AntiHeadshot on December 12, 2012, 01:58:00 PM
found this http://web.chemdoodle.com/demos/2d-to-3d-coordinates (http://web.chemdoodle.com/demos/2d-to-3d-coordinates) think this will help me, but i cant figure out how to get lines without something on the end. Like on the lower part of the pentagon at the N. Are there "hidden" elements?

Edit:
Also noticed building it would be realy fragile ... I think I will follow your advice and take it as a picture.
Title: Re: Turn 2D structure into 3D (Leucine, Pyrrolysine, Valine, Glutamic Acid)
Post by: curiouscat on December 13, 2012, 04:07:13 AM
found this http://web.chemdoodle.com/demos/2d-to-3d-coordinates (http://web.chemdoodle.com/demos/2d-to-3d-coordinates) think this will help me, but i cant figure out how to get lines without something on the end. Like on the lower part of the pentagon at the N. Are there "hidden" elements?

Those are Carbons.
Title: Re: Turn 2D structure into 3D (Leucine, Pyrrolysine, Valine, Glutamic Acid)
Post by: Babcock_Hall on December 13, 2012, 05:29:53 PM
The twenty common amino acids, and some of the less common amino acids have both three-letter and one-letter abbreviations.  The one letter symbol for glutamate (Glu) is E.  O is the abbreviation for pyrollyisine;  http://www.ddbj.nig.ac.jp/sub/ref2-e.html  In other words, your tetrapeptide is LOVE in the one letter coding system for the amino acids.

If you want to build a model of a peptide, which is the general class of molecules to which your example, LOVE, belongs, I have done a similar exercise (a tripeptide made of three alanine residues, namely Ala-Ala-Ala or AAA) with a type of molecular model kit called Cochranes models.  Sigma-Aldrich sells a kit that was designed with biochemistry (peptides and DNA) in mind.  They are not particularly cheap; however, you could assemble a model without any more information that you already have.  BTW, chemists are very clever or very lazy when they draw things.  Not all of the hydrogen atoms are shown in the drawing you provide (because there are rules that govern how many there must be), and the vertices are carbon atoms, as curiouscat said.

The true three dimensional shape of a short peptide such as yours is very hard to predict, and is probably a family of many shapes that interconvert.
Title: Re: Turn 2D structure into 3D (Leucine, Pyrrolysine, Valine, Glutamic Acid)
Post by: curiouscat on December 13, 2012, 10:54:50 PM
The true three dimensional shape of a short peptide such as yours is very hard to predict, and is probably a family of many shapes that interconvert.

Does something like Rasmol or VMD or Gaussian do a good job at this?
Title: Re: Turn 2D structure into 3D (Leucine, Pyrrolysine, Valine, Glutamic Acid)
Post by: discodermolide on December 14, 2012, 02:42:44 AM
here is a 3D energy minimised picture of it.
I don't know if it will help you ???
Title: Re: Turn 2D structure into 3D (Leucine, Pyrrolysine, Valine, Glutamic Acid)
Post by: aHerraez on April 14, 2013, 11:15:59 AM
You can draw the 2D structure and get a 3D yourself at (...)

For example, these are 2 images generated from a 3D model in MOL format (attached). What file format could you use? It is possible to export to other formats, like VRML, PovRay.
(https://www.chemicalforums.com/proxy.php?request=http%3A%2F%2Fs24.postimg.org%2F47ft3tza9%2FLOVE_spheres.jpg&hash=16ee581e0efcd27c0e5b9bc04e84b9b1) (http://postimg.org/image/47ft3tza9/) (https://www.chemicalforums.com/proxy.php?request=http%3A%2F%2Fs9.postimg.org%2F5tl4xgzu3%2FLOVE_ball_stick.jpg%5D&hash=f24ee563f0b03dd46bc8cbd62961a4fe) (http://postimg.org/image/5tl4xgzu3/)
Title: Re: Turn 2D structure into 3D (Leucine, Pyrrolysine, Valine, Glutamic Acid)
Post by: Borek on April 14, 2013, 04:11:07 PM
You can draw the 2D structure and get a 3D yourself at (...)

Sorry. I believe you posted in a good faith, but I don't like the idea of linking to pages with Java applets, especially now, soon after Java related security problems.