Molecular visualization software

[SeeingRed]

Can anyone recommend one (not command line) that is particularly well-designed or useful? I've used VMD for some basic protein renderings, but it seems to be built for much more heavy duty stuff than what I need. I'd prefer one that runs under Mac OS X, especially if it's Mac-only, but Windows is fine too.

[jeniferdesauza]

The most up-to-date list of additional resources is in the relevant section of the World Index of Molecular Visualization Resources, //molvisindex.org//. Chemscape Chime from MDL Information Systems, Inc., allows rotating a molecular image within a Netscape page. Multiple molecules can be displayed within a single web page, unlike helper applications (such as RasMol) which display each molecule in a separate window. Chime also supports scripts (using a superset of the RasMol scripting language).

[Tall Chai Latte]

A very simple one I've been using for a long time is PyMOL. It's also capable of making movies and such, but if you just want to look at protein structures (e.g. open up a pdb file) and stuff like coloring polypeptide chains, this should suffice. It comes in Windows and Mac (called MacPyMOL) versions. I've also used MOLMOL and RasTop but unsure if the later one is still available for download. Hopefully this is what you are looking for..

[Apt86]

How About trying UCSF Chimera

Can anyone recommend one (not command line) that is particularly well-designed or useful? I've used VMD for some basic protein renderings, but it seems to be built for much more heavy duty stuff than what I need. I'd prefer one that runs under Mac OS X, especially if it's Mac-only, but Windows is fine too.

[Eigen]

MOE (Molecular Operating Environment) is what our group uses- it's quite robust, and does visualization as well as calculations/simulations. We use this to modify either the environment (you can solvate/desolvate, change ion concentrations, etc) and check the new structure/stability, or to mutate the protein and check new structures/stability. It's also what I use to make all of my figures for papers and such, since you can take existing pdb files and modify them (ie, take GFP and split it to show a split reporter protein).

If you just want to be able to manipulate peptide chains (say, from a pdb file) the "protein workshop" software that you can download from the PDB website does that- you can turn chains on, off, and color them differently.

Edited February 12, 2011 by Eigen