Hi there,
I would like to start a thread on computer programs that people for research. Please include what you use and why, and why you use it over any other options. Maybe people can learn about some options that are out there that they weren't aware of. Lets see where this goes.
I'll start:
In our lab we mainly use the standard ones (chemdraw, powerpoint, excel, word). We also like using MestreNova for processing NMR, because we can purchase perpetual licenses, and move them from computer to computer as old members leave and new members join. They have pretty good customer service, and it's very user-friendly and works on Macs, PCs, and linux machines, which is a plus. For a while we had all three computer platforms in our lab, and it was nice to have a program that everyone could use.
We generally use Mercury for looking at cif files, and that works pretty well, and is free.
Once in a while there is a discussion about using Endnote for writing papers and theses, but we haven't really followed up on it. Does anyone use endnote regularly? Once in a while someone mentions using gNMR and igor, but they aren't used with any frequency.
I use EndNote and can't imagine having written my PhD thesis or any of my publications without it. I have run into some problems with automatic downloading of references and the meta tags get messed up, so be careful to check your refs before you hit "submit" or your reviewer will have a fit.
I have used gNMR a lot for VT NMR work, but we only fire that up every couple of years.
I have started using "Papers" to organize pdfs (I think Mac only) and Evernote to take notes at conferences.
Oh, and Dropbox to archive and back up current files in the cloud. Things like current drafts of proposals and papers.
I've recently found Dropbox to invaluable for my thesis and for working on papers with my advisor. If anyone wants to sign up (its free), let me know and I can refer you and we'll both get 250 MB of extra space (heh, blantant selfishness, i can't say no to free stuff).
Also, as far as NMR processing goes, the Global Spectrum Deconvolution (GSD) tool in MestreNova is pretty darn cool, and useful for getting integrations of overlapping peaks or deconvoluting complicated resonances. Check out their website. It might be useful to get a perpetual license for mestrenova if you are looking for a good NMR program with good support.
We basically tossed the idea of getting endnote up and running, its more of something you should start when you first start doing research on a project rather than later down the line.
I am a huge fan of Endnote. Started using it as a grad student, and, like Adam, I can't imagine writing a paper or grant without it. Smith used to support it, but now has switched to RefWorks. I hear good things about RefWorks, but it never seems like a good time to make the switch. At some point I may just bite the bullet and try it.
I've used Dropbox a little and have liked it. I've also stared using Papers to read/organize journal articles. So far I really like it. As one colleague said, "it's the first program that's made me think I might actually be able to get rid of those file cabinets full of articles someday."
For crystallography I like the WinGX Program System.
http://www.chem.gla.ac.uk/~louis/software/wingx/
From the web site: "WinGX is a MS-Windows system of programs for solving, refining and analysing single crystal X-ray diffraction data for small molecules. It provides a consistent and user-friendly GUI for some of the best publically available crystallographic programs, and has interfaces to other popular programs such as SHELX-97 and SirWare programs (SIR-97, SIR-2004)"
For nmr I prefer SpinWorks:
http://www.umanitoba.ca/chemistry/nmr/spinworks/
It can do lots including spectral simulations and DNMR.
Both are free.
I had not heard of the WinGX program system, thanks for mentioning that!
I recently played around with Jmol and found it somewhat interesting. I just wish that exporting video/animations from it was easier (i was able to use a video-capture program to get a .avi of a rotating molecule in Jmol).
Kyle, I really like Jmol because we have a Jmol plug-in for our campus Moodle. (I know that may sound like the Charlie Brown Adult Voice -wah wah wah wah wah - to some people.) So, I can put up lots of cool structures for students in my chem courses to look at and rotate in Jmol. This is helpful for referring to in problem sets and other in-class activities, especially involving symmetry! All I need to do is create a .pdb file of the structure I want and then upload it to the Moodle.
Now, what I REALLY want is for Jmol to work on the iPhone or iPad! But that is asking a lot...
Have you seen "Molecules" for the iphone/ipad? I downloaded the iphone version but its lacking many tools I would like to use. If they had designed it better it could a wonderful app. Basically its only good for showing the preloaded molecules and you can only add compounds from a known server (I honestly haven't tried adding any molecules to it yet). I think the source code is available so maybe someone could design a better version (hmmm... maybe a computer science student could do it for a senior project??).
Still, you might find it useful.
Here's the link for it:
http://itunes.apple.com/us/app/molecules/id284943090?mt=8Dr. Kyle Grice Post-Doc UCSD Kubiak Lab
Actually, I just played around with my iphone and molecules and found this website with a bunch of pdbs, you click to them on your safari in the iphone and it prompts you to open them in molecules. Unfortunately some of them aren't properly made and are missing bonds, but the spacefilling models still look good.
Heres a database of pdbs:
http://www.uwsp.edu/chemistry/pdbs
Dr. Kyle Grice Post-Doc UCSD Kubiak Lab