Dan, I think it's fair to say that PyMOL's currently molecular building capabilities are at the stage of a technology demonstration/proof-of-concept, but very little effort has yet been expended toward making them useful for real work.
Part of that is because we don't yet have a general back-end modeling engine inside of PyMOL (molecular sculpting is a pure "GIGO" kind of thing). That is still an important long-term goal. But the other reason is that I don't really have a clear idea in my mind for how such a builder should operate. What I would like to get from you and all other interested PyMOL users are wish-lists for how PyMOL's molecular builder should work (better). No hurry though -- feedback over the next month or two should be fine, and anyone attending MUG or CUP is welcome to give me an ear-full next week. Basically, a major goal is to evolve PyMOL into a builder that can be useful across the board for biology and drug discovery: for proteins, small molecules, nucleic acids, carbohydrates, solvent, and so on. As a general tool, it should be capable of supporting crystallography-oriented building, manual homology modeling, and hypothetical "hand modeling" of small molecules, as well as simple illustrative tasks such as the one you're working on. Of course, specialty tools like "O", "Quanta", "Modeller", and "MacroModel" will always be superior in their respective niches, but I hope PyMOL can become eventually become "good enough" for simple common molecular building tasks... Questions to consider: What are the best builders out there today that we should learn from? What are the key functions PyMOL must absolutely have to be a builder? What other extra attractive feature should PyMOL seek to emulate? How can we make the best use of what is already in PyMOL, unique or otherwise? What are the biggest "holes" in the current versions? Things that are already on the radar: Rotamer-libraries. A 1-D sequence viewer with alignment and editing capabilities. An integrated builder tutorial. Finding an existing force-field provider to work with... Back and forth 2D to 3D for small molecules. Dan, It sounds like a feature you would like is that ability to aim the chain being built towards a certain direction. In the meantime, to accomplish your task, build the chain first, then turn on Auto-Sculpting in the Sculpting menu, put the mouse into editing mode, then control-left-click-and-drag to move the chain where you want it to go. Ctrl-middle-click to pick one (or more -- in the latests betas) joints...and then shift-left-or-middle click-and-drag, or control-left-click-and-drag to move the resulting fragments. If your chain is small, increase the number of Cycles per Update to accelerate convergence. Cheers, Warren > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Moriarty, Daniel > Sent: Thursday, February 19, 2004 9:47 AM > To: email@example.com > Subject: [PyMOL] using the build function > > Hello everyone, > > I'm trying to build some model proteins for a diagram showing > a protein unfolding over several steps. I'm using the build > function in the 0.95beta10 release. The main problem is that > I can't control the angle of the protein chain, so the chain > just goes off in one direction only, unless proline is placed > in the middle of a helix at which point it goes off at a new > angle. This makes me think that it can be specified, but I > just don't know how to do it. > > > Any help would be appreciated, > > Dan > > > > ------------------------------------------------------- > SF.Net is sponsored by: Speed Start Your Linux Apps Now. > Build and deploy apps & Web services for Linux with a free > DVD software kit from IBM. Click Now! > http://ads.osdn.com/?ad_id56&alloc_id438&op=ick > _______________________________________________ > PyMOL-users mailing list > PyMOLfirstname.lastname@example.org > https://lists.sourceforge.net/lists/listinfo/pymol-users >