Hello, Like others, I am new to Pymol. I am interested in seeing if a small molecule (.mol2) "ligand" has a binding site on one of two proteins (2KAV and 5FEB) but since they are known to interact, it might be something between the two. While I am also looking into/learning Autodock Vina, in Pymol I tried pulling up one protein (successful), then the other (successful) and interestingly they came up somewhat "intertwined" next to each other. Then I brought in the small molecule (300MW) and it jumped to an orientation with one end next to an a.a. of one protein and the other end next to an a.a. of the other. And some of the side groups made possible sense (e.g. H-bonding). No matter which order I pull up the proteins or molecule, they always configure this same way.
So my question is ... are these alignments just fortuitous? (then why the same each permutation of adding) or is Pymol suggesting an optimal alignment for the 2 proteins and "suggesting" a binding site for the small molecule? Is there a better way to look at this? Thanks for any insights! Larry (pymol newbie)
_______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
