Molecular diagramming software

[Kirk Keyes]

I'm looking to see if people here have any experience with molecular diagramming software. What have you tried, what do you like, and most importantly, I'm hoping suggestions are for free or very inexpensive packages.

I've looked at Marvin - from http://www.chemaxon.com/
It's free with basic functionality, more if you can get an academic license.

Kirk

 

[keithwms]

I used to use "weblab viewer pro" from accelrys; I don't know how it'd compare to what you mention. I think they renamed it but as I recall there is a freeware viewer.

http://accelrys.com/products/discovery-studio/

What's your application? Is it just visualization or are you doing minimizations etc? Mostly I used the accelrys stuff to make structures for further QM minimization by DFT or such and to visualize different regions of biomolecules etc. For that I need to be able to look at pdb files and the accelrys stuff was good for that.

 

[Kirk Keyes]

Keith - I'll look into that.

It's pretty basic functionality I'm looking for - just for use in printing/publishing/web use. No really chemistry calculations. Certainly for drawing some reactions. But it gets really hard to draw (well, I can't draw, that's why I photograph) these out and have them look good/professional. And there's only so much one can do in ASCII with chemical equations.

 

[Photo Engineer]

Just get an organic chemistry template Kirk and use that. That is what I used to use.

Hexagons, pentagons, triangles and etc. You are all set. Problem is, I had 2 or 3 of them and can't find them now. So, I'm stuck too.

PE

 

[Kirk Keyes]

Templates - you mean those plastic things with holes in them that you run the tip of your pencil around inside the holes? I've got some of them, not specifically for organic chemistry, but how do I save the output from the template into a jpg, png, or svg? Remember, one of my product specifications was that the output needed to look professional. If I'm drawing it by hand, it will not look professional...

 

[dwross]

Kirk,

Here's something that might work.

http://www.download.com/ACD-ChemSketch-Freeware/3000-2054_4-10591466.html

d

 

[ic-racer]

I have used "ChemDraw" since the 80s. It still runs on my older iMac. Looks like they are still in business and they have some free stuff to try:

Dead Link Removed

 

[Photo Engineer]

Templates - you mean those plastic things with holes in them that you run the tip of your pencil around inside the holes? I've got some of them, not specifically for organic chemistry, but how do I save the output from the template into a jpg, png, or svg? Remember, one of my product specifications was that the output needed to look professional. If I'm drawing it by hand, it will not look professional...

Kirk;

Scan it.

That was all I had in the 60s and 70s and I used it for my thesis. It does a fine job for organic synthesis and if I had mine, I could draw some fancy suff to post.

I'm looking locally for a set and also looking for my old one.

PE

 

[Struan Gray]

You could use a template on a graphics tablet I suppose.

I don't do much chemistry, and when I do it tends to be inorganic -), but when I have needed to draw molecules I just used the polygon and isometric drawing tools in a good drawing program (Canvas from Deneba Software is my catch-all, but I think Illustrator will do this equally well).

I used ChemDraw way back when. It was excellent, but I've not used a recent version.

 

[frdrx]

From the realm of Free Software, there is Easychem. GChemPaint is another.

 

[keithwms]

I agree with ic-racer, chemdraw is good. The problem I have with several of the fancier visualizer programs is that they can't spit out textbook-simple skeleton diagrams. Chemdraw can do that and it's relatively intuitive.

 

[Kirk Keyes]

Denise - I did try ACD Chem Sketch - but not for long. That could work I think.

ChemDraw - looks cool, but man, is it expensive. Or did I miss the cheap version.

 

[Kirk Keyes]

From the realm of Free Software, there is Easychem. GChemPaint is another.

Well, I see that's not only free as in beer, but free as in speech.\

If I was running Linux on a desktop (only servers at this point) I'd use them. Thanks.

 

[Lee L]

If I was running Linux on a desktop (only servers at this point) I'd use them. Thanks.

Assuming the computer you're on is your own, it's not that difficult to install linux to dual boot, giving you a choice of operating systems at boot time. Newer versions of linux can read/write MS Windows NTFS files so you could save bitmap or EPS output to your Windows partition if you needed that.

Both gchempaint and easychem are in Debian repositories, and appear to be in repositories for many other distributions as well, so it would only be a couple of mouse clicks to install.

Monetary cost and restrictions on usage are zero, and it wouldn't take much time.

Lee

 

[Kirk Keyes]

Lee, I'm quite familiar with Linux. I actually got a Linux System Admin certificate back in Y2K.

 

[Neanderman]

I've used MDL ISIS/Draw (now part of Symyx).

http://www.mdl.com/downloads/index.jsp

It is a "no-fee" download.

I'm not very good with it, but it seems to have good capabilities.

Ed

 

[Kirk Keyes]

Thanks - I'll check it out. I've been playing with Marvin Draw some more, and it does what I've asked so far fairly well.