Friday, 27 November 2009

TwirlyMol (2)

It looks like I cannot show more than two molecules on one page. Here is the third one I wanted to show (you may have to click the header of this post to see it):

For molecules that are not in their data base I can enter the molecule as InChI (which I can create through open babel).

This is the molecule of my Master's thesis [2,2'-bipyridyl]-3,3'-diol with the InChI 'InChI=1/C10H8N2O2/c13-7-3-1-5-11-9(7)10-8(14)4-2-6-12-10/h1-6,13-14H'.

[To correctly translate it into a form that the browser interprets correctly, I can convert it on their homepage (I enter the InChI and take the converted one from the link it produces). Then it looks like this: 'InChI%3D1/C10H8N2O2/c13-7-3-1-5-11-9%287%2910-8%2814%294-2-6-12-10/h1-6%2C13-14H']
[Edit:] The problem was that I did not put the 'InChI=' prefix and it is not necessary to do this conversion.




In fact the molecule should be all in one plane and have intramolecular hydrogen bonds but it is still cool that the tool can create the structure from just one line.

5 comments:

Markus Sitzmann said...

Hi Felix,

nice too hear that you like TwirlyMol coming from our Resolver.

Some comments:

It should work with more than two structures at the same page - and in fact, I see all three structures at the sime time on you blog. There might be the case that the whole things sometimes get stuck - unfortunately it is quite tricky to find the reason (I am still surprised that it works in blogs anyway)

Instead of InChI you can also use arbitrary SMILES string.

And I wonder why your InChI didn't work directly. I copy/pasted it from your blog and it worked as it is - the only thing you need to do is the addition of the "InChI=" prefix which is required by the InChI format specification (and makes life easy to recognize them).

Markus

Felix said...

Hi, yes it is kind of strange: in firefox I see the 2nd and 3rd molecule, in explorer it's the 1st and 2nd. but i never see all of them, i don't know

and yes, i think i left out the InChI= prefix, so I guess that's why it did not work

baoilleach said...

Hey Felix - it seems to work fine for me too. If you've got time, could you open the error console in Firefox (under Tools), click on Clear, and then reload the page. If you could send me or Markus a screenshot of any errors, that might help.

baoilleach said...

Now with added fog, nicer spheres, and fewer error messages(!).

Felix said...

alright ...