FYI / FTR -- my recent post on the Jmol list pertaining to feature duplication & interoperability.
-----Original Message----- From: jmol-users-boun...@lists.sourceforge.net [mailto:jmol-users-boun...@lists.sourceforge.net] On Behalf Of DeLano Scientific Sent: Wednesday, March 05, 2008 12:34 PM To: jmol-us...@lists.sourceforge.net Subject: Re: [Jmol-users] Pymol, DSV, and Jmol > There are a couple of features that pymol and DiscoveryViewer have > that doesn't seem to be in Jmol. Can anyone comment if they do exist, > or if someone is working on them. Just a general comment: while I am wholly in favor of sound UI concepts being universally adopted, I do think there is the potential for misallocation of limited open-source development resources for the Jmol and PyMOL projects in terms of recreating similar or identical functionality within the two packages. Jmol and PyMOL are both unrestricted open-source projects, under LGPL and BSD-like licenses respectively. As such, they are both part of the permanent code commons available to everyone for adoption and use in derivative projects. It is no accident that Jmol and PyMOL have excelled at different tasks, with, for example, PyMOL staying out of the browser and Jmol off the GPU. Indeed, there is little point in open-source projects competing directly, and it is clear that complementarity of efforts has produced multiple distinct benefits for users. Consider for a moment Jmol's in-browser capability & robust platform independence juxtaposed with PyMOL's OpenGL graphics performance & ray-traced rendering quality. Both are valuable in their own way, and much the same can be said for other related open-source projects (e.g. Coot, cctbx, clipper, openbabel, etc., each it their own area of specialization). So if indeed our projects are now or are in the future blessed with such an excess of development resources that we can afford to duplicate each other's efforts, then wouldn't it instead make a whole lot more sense to direct such resources toward advancing interoperability between projects rather than risking stagnant or wasteful redundancy? I do think it would be a wonderful thing for all of our users if people could transparently move dynamic molecular content & visualizations back and forth between PyMOL & Jmol. Though this idea is far easier stated than implemented, if we could get even just two leading open-source molecular visualization packages speaking a common molecular tongue, then surely other packages would eventually learn to speak it as well. Software interoperability remains such a horrendous unsolved problem for the field! Food for thought. Cheers, Warren ________________________________ From: jmol-users-boun...@lists.sourceforge.net [mailto:jmol-users-boun...@lists.sourceforge.net] On Behalf Of Robin Emig Sent: Tuesday, March 04, 2008 9:34 AM To: jmol-us...@lists.sourceforge.net Subject: [Jmol-users] Pymol, DSV, and Jmol There are a couple of features that pymol and DiscoveryViewer have that doesn't seem to be in Jmol. Can anyone comment if they do exist, or if someone is working on them. 1) PyMol has that great object/selection/etc list on the right hand side, where the user can quickly change the color, style, etc of everything displayed 2) Pymol has a "mutation" wizard (actually so does a Package called KiNG), where you can select a residue, mutate it, and rotate through all the rotamers, in addition it will show collisions as red circles 3) DSV has a "Hierchy" window, a simple tree browser showing the chains, amino acids, atoms. Which allows selections 4) PyMol and DSV both have a "sequence" view If these do not exist in Jmol as of now, are they within the scope of Jmol, or should projects like Bioclipse, Strap, or other be the places this functionality should exist in. ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list jmol-us...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
