On Sat, 9 Feb 2002, Jacob Corn wrote: > First off, let me congratulate Dr. DeLano for creating such an > amazingly useful program. The combination of GUI and command-line is > great, making it easier to use than MolScript and more functional than > DeepView. Not to mention the *very* polished graphics that it is > capable of producing.
Can I quote you on that? Seriously. A web page containing genuine endorsements from well-respected scientists might help others get over the PyMOL activation barrier by encouraging them to learn the program. If anyone else would like to submit a candid quote for the web site, then please email me directly in order to avoid unnecessary list traffic. I'll put something up if 9or when) I get about a half-dozen responses. These quotes shouldn't be just praise -- honest identification of strengths and weaknesses would do more to inform potential users. Thanks for making my day! Molscript and DeepView are awesome programs, so it's very satisfying to hear someone other than *myself* suggesting that PyMOL might be able to compete in their league. > For an upcoming talk we'd like to show some footage of our molecule of > interest rocking along the y axis (thus swinging back and > forth along some putative sites on the "top" of the protein). > I'm assuming there's a way to do this, but I'm not sure exactly how to > do so. I took a look at the mrock function in movie.py, and noticed that, > while > one passes it 5 arguments from the command line, there are actually 6 > variables in the function, the last one being "axis," explaining my > inability to pass the function an argument for the axis of rotation. > However, in my desperation, I've even gone so far as changing this last > variable to > axis='y' within movie.py itself, but the molecule continued to rock on > the x axis. Any suggestions? I'm puzzled -- the current version of movie.rock rocks about the Y axis by default, but that is easily changed as shown below. Note the use of a named argument in order to override the default value for the 6th argument while skipping over the 4th and 5th arguments. That flexibility is part of the reason I love Python. # first, just load something, define, and play the movie... fragment phe mset 1 x30 mplay # x-axis movie.rock 1,30,15,axis=x # y-axis movie.rock 1,30,15,axis=y # z-axis movie.rock 1,30,15,axis=z #--- Jacob, are you using the current version 0.78? If not, then perhaps there was a problem with an older version which has been fixed. By the way, if you are using straight Python instead of the PyMOL command language, then you need to add back the quotes and parentheses: from pymol import movie movie.rock(1,30,15,axis='y') Cheers, Warren
