Re: [Jmol-users] switching molecules in a sdfile

[<osr...@ch...>]

Hi Dominik,

I only sent my link to illustrate the concept. You could do this via the 
Jmol applet from a page on your server. I'm not sure about the Jmol 
application.

The only Jmol method for doing this is on line. Four remote options come 
to mind:

1) NCI/CADD Chemical Identifier Resolver
http://cactus.nci.nih.gov/chemical/structure

Since Jmol creates a SMILES for any molecule in the window, queries of 
the following type send by Jmol will do the trick:

http://cactus.nci.nih.gov/chemical/structure/CCCCO/image

Since Resolver computes these images, the resource is almost unlimited 
in its ability to generate 2D structures. Query parameters also allow 
gif image modification.

2) PubChem

3) ChemSpider

PubChem and ChemSpider can also be automated via Jmol, but this is a bit 
more difficult. SMILES from Jmol need to be converted to InChI or 
InChIKey. This can be done by using a resource on Chempider or by using 
Resolver to do the SMILES conversion. If you want to see this is a 
non-Jmol context go to:

http://chemagic.com/aka/

In the above application I am grabbing 2D images from ChemSpider or 
PubChem per user choice. These images are limited by the database nature 
of PubChem and ChemSpider, but there are still millions available.

4) OPSIN
http://opsin.ch.cam.ac.uk/

OPSIN is super slick! BUT it computes by IUPAC only. HOWEVER this is 
really neat and powerful:

http://opsin.ch.cam.ac.uk/opsin/2-butanone.png

Just incredible!

If you want to pursue details on any of these via your server and Jmol, 
let me know and I'll be more code specific.

Otis


On 9/30/2011 11:23 AM, Dominik Haferkamp wrote:
> Thank you!
> With an old version i don´t get it(i haven't notice i had one) but with the new one it works.
> But now i have a problem with this site you send me.
> That is what i mean, but is there any way to do it offline?
> I have many molecules in the sdf file and i need a Image of all. When there is a way by linux terminal i can write a small skript and  I do not need to do it by my self.
> There is a second Problem:
> On the site i can´t use my own files. When i click on file there is only "reload" and the three first "save ..." everything else is grey.
>
> Thank you for your fast Help
>
> -------- Original-Nachricht --------
>> Datum: Fri, 30 Sep 2011 10:16:06 -0400
>> Von: "osr...@ch..."<osr...@ch...>
>> An: jmo...@li...
>> Betreff: Re: [Jmol-users] switching molecules in a sdfile
>> Dominik,
>>
>> The command "frame all" will show all the molecules. The commands "frame
>> 1," "frame 2," etc will allow you to select.
>>
>> On the second question, try the following:
>>
>> 1) Go to http://chemagic.com/web_molecules/script_page_large.aspx
>> 2) Click Image Capture
>> 3) Click NIH 2D Capture
>>
>> If that's what you're looking for, send me a note, and I'll explain how
>> to do it.
>>
>> Otis
>>
>> On 9/30/2011 9:54 AM, Dominik Haferkamp wrote:
>>> Hello
>>> i have some molecules in a sdf file. How can i switch between the
>> molecules?
>>> jmol shows me only the first. But i have to see the other too...
>>> And my second question is, how i can make a 2d structure formula with
>> Jmol?
>>> Thanks for your Help
>>>
>>>
>> -- 
>> Otis Rothenberger
>> chemagic.com
>>
>>
>>
>>
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-- 
Otis Rothenberger
chemagic.com