Figure 1. My favorite protein's active siteNo more pyMOL for me. I have now been converted to the wonders and joys of using VMD. Not only is it free but the user-friendlyness of this program is astounding. It, to my knowledge, has the same sort of capabilities as pyMOL (i.e. alignments, distance determination, etc.) and can still be used with python (if you are so inclined).
If you are like me and are not a hardcore crystallographer but still want to be able to quickly generate awesome looking structure figures from pdb files or just want to see the relative positioning of residues in protein active sites, then VMD is amazing...
3 comments:
LOL! What took you so long? VMD has been around for like ten years longer than PyMOL!
Yea, but PyMOL really is open-source and ships with several versions of Linux. VMD is more like Microsoft shared source: you can look, you can touch, but you sure as hell cannot redistribute (inside Linux, etc.). Also VMD isn't really free: it has cost U.S. taxpayers million$ wheras PyMOL's only funding comes from people who actually use it. Anyway, they're different and both good at some things. Say have you tried Chimera from UCSF? Now that's a really easy to use program! It kicks both PyMOL's and VMD's butts IMHO.
I just downloaded Chimera the other day, but haven't had a chance to play with it yet. Problem is, once I get going with a program, I usually am reluctant to try something new (which is why I still use Microsoft office-which I do believe is an instrument of the devil-- instead of LaTex)but I will have to check it out...
Post a Comment