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Chemical structure/formula softwares?

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Chemical structure/formula softwares?

Postby hurly » Fri Mar 21, 2008 10:29 pm

Hello all scientists!

I remember WORD having a built-in plugin/menu for typing chemical structures/formulas.
Other than that, what do you guys recommend as other softwares for drawing chemicals? It would be nice to have the possibility to render out 3d molecules as well.

Thank you.
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Re: Chemical structure/formula softwares?

Postby MichaelXY » Fri Mar 21, 2008 10:43 pm

Check out this link.
http://www.geocities.com/athens/thebes/ ... ewdraw.htm

I think JMOL is what you want for 3D molecules.
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Postby hurly » Fri Mar 21, 2008 10:50 pm

Thanks for the quick reply. I will check out the links!
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Postby MichaelXY » Fri Mar 21, 2008 10:52 pm

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Re: Chemical structure/formula softwares?

Postby blcr11 » Sat Mar 22, 2008 6:54 am

How fancy do you need? My favorite structure drawing program is ChemSketch from ACD Labs. There are commercial and freeware versions available. The program is fairly easy to use and will do some sophisticated drawing (Buckeyballs, for example). I believe you can copy and paste drawn structures directly into a Word document. It's 3-D rendering is OK but limited, and you can only go so far in trusting its energy minimization (it's not really a computational chemistry program--for that you have to pay money). Check it out at http://www.acdlabs.com/

PyMOL is an opensource program that does publication-quality 3-D rendering. There will be a steep learning curve if you've never used a program like PyMOL before (such as rasmol, for instance). You can use PyMOL to build molecular structures, but I don't think you can create a 2-D structural formula. Like ChemSketch, PyMOL is not a computational program. If you need real energy minimization you need to use another program. You can find PyMOL at http://pymol.sourceforge.net/

There's nothing wrong with Jmol either. It is intended mostly for screen displays.
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Postby MichaelXY » Sat Mar 22, 2008 7:31 am

Wow that looks cool, I just DL the freeware version of ChemSketch. I am gonna give a test spin.
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Postby hurly » Sat Mar 22, 2008 10:29 am

I googled a bit and found out about ChemOffice Ultra. Is it a recommended software? There's also a ChemBioOffice Ultra, but I'm not sure what the difference is.


Edit:
I have another question that I would like to ask. While I was a student, we had access to a database containing chemical properties to the chemical that we searched for. I don't remember the name of it, but does it exsists similar databases out there?
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Re: Chemical structure/formula softwares?

Postby blcr11 » Sat Mar 22, 2008 1:57 pm

ChemOffice is a suite of programs that includes ChemDraw and a small host of other types of programs. It's a great program, but it isn't cheap. I think you can download a demo. You may be able to purchase ChemDraw as a standalone program just for drawing structures, but I'm not sure. The drawing capabilities of ChemDraw and ChemSketch are similar.

Both ACD Labs and CambridgeSoft (makers of ChemOffice) have molecular properties calculators. It is a limited function in the freeware version of ChemSketch. I don't know of any completely free version of these kinds of databases. The properties of elements can be found on any number of web versions of the periodic table, but I don't think that was what you were looking for.
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Postby blcr11 » Sat Mar 22, 2008 2:41 pm

Well, I may have to retract what I said. There are a number of public databases available. I don’t know if they will cover exactly what you’re looking for. Many seem to be created to serve the environmental sciences.

http://webbook.nist.gov/chemistry/
http://chem.sis.nlm.nih.gov/chemidplus/
http://www.gsi-net.com/UsefulTools/Chem ... seHome.asp
need subscription for full access to: http://www.chemnetbase.com/
http://library.dialog.com/bluesheets/html/bl0303.html

A links page: http://www.lib.berkeley.edu/CHEM/properties.html
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Postby blcr11 » Sat Mar 22, 2008 2:53 pm

I'm not familiar with the ChemBio version. I imagine it is for viewing and modifying larger structures like peptides and proteins. ChemDraw probably has a limit for the number of atoms it can display. ChemBio will have a much higher limit in the number of displayable atoms, but will probably not have a superflexible drawing capability. The full suite of ChemBio may have a minimization program built in. Other software for dealing with both large and small molecules are Moe and some of the Accelyrs programs--both are on the expensive to very expensive side.
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