David, Some good suggestions, but I think too localized to you, specifically. My comments follow.
> 1) I would love it if the PDB Loader Service Plugin would clean up what it > left in /tmp on pymol exit. I have a feeling this might be complicated > though. I just have a bad memory when I first entered this world and I had > pymol open and I was trying to load a pdb and the plugin just would not work. > The previous graduate student using the system had previously loaded the > same pdb using the plugin and the file had written in /tmp and the PDB Loader > would therefore not get me the file. When you're just starting a rotation in > a new lab, that type of problem can scar you as you have to explain why it > took you half an hour to open a pdb in pymol... First time I've heard this request. PyMOL attempts to cache the data, so you don't have to keep re-downloading the PDB files. Also, if PyMOL crashes or is suddenly killed, there's no way to clean up the remaining PDBs. Plus, there could be security issues with removing files: "fetch '/bin/rm -r *'" might allow for some kind of evilness. To be serious about this, many more people need to show interest in it. > An alternative solution is to check for the filename before trying to write > there. And be like Firefox and just name them 1ACB-1.pdb when 1ACB.pdb can't > be written to. Maybe this smacks of a different solution altogether: project-based sessions? > 2) This might be out of your range as it is a plug in written by the > community, but DynoPlot could become something really cool with a little love > and care. My big problem right now is that you are only able to create a > plot with a single selection. I teach a lab once a year where we have the > students use dynoplot to make ramachandran plots of the helices, then they > have to restart pymol before they can select the beta sheets and make a > ramachandran plot of them as well. As we all know, losing a pymol session > can be a painful experience. Having to restart is also rough. You would have to work with the DynoPlot author to improve this. > 3) A more extensive undo/redo system. It would be nice to be able to undo > anything. And then redo it. I'm talking "fetch 2no8; split_states", > realizing there's 60 models and just doing "undo" and having a single model > again. Or I accidentally change my view, I can go back. I don't know what > level of granularity it should be, but something would be good. Again, > losing that perfect view or such can be painful. This is a definite must, especially for molecular editing. In PyMOL, sadly, this is very hard. Warren fretted about this for months, and even started a basic level of undo. I predict this will be around after we do some major refactoring--possibly in PyMOL 2.0. :-) Thanks for your suggestions. -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
