Hi Emily, PyMOL's morphing performs two steps: (1) RigiMOL, and (2) refinement of non-backbone atoms by sculpting. The second part can be skipped with "refinement=0".
Unfortunately, there is no RigiMOL publication or method documentation. The sculpting refinement tries to avoid clashes and maintain the local sidechain geometry, based on start and end conformation as references. You are right that sculpting doesn't consider the Ramachandran plot or a real energy force field. But it does consider clashes (it has a VDW term). Check "Build > Sculpting > ...", the bottom part of that submenu lists some of the available terms. The corresponding numerical values can be found here: https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/Sculpt.h The "morph" command refinement uses all sculpting terms. You could customize that, e.g. exclude VDW repulsion, like this: PyMOL> morph mout, sele1, sele2, refinement=0 PyMOL> from epymol.rigimol import refine PyMOL> refine(5, "mout", sculpt_field_mask=(0xFFF & ~0x60)) You can also "fix" atoms, e.g. all non-polymer atoms, like free ions, which tend to bounce around as a result of the refinement: PyMOL> morph mout, sele1, sele2, refinement=0 PyMOL> from epymol.rigimol import refine PyMOL> flag fix, (not polymer), set PyMOL> refine(5, "mout") Hope that helps. Cheers, Thomas On 30 May 2016, at 12:43, Emilia C. Arturo (Emily) <ec...@drexel.edu> wrote: > Hello. > > I would like to know more about the type of interpolation that is done when > morph is called, and what calculations are done at each refinement cycle. Is > there a literature reference or previous forum discussion to which you can > point me? > > From my sifting through the internet, I settled on the likelihood that > refinement is done using the "molecular sculpting" algorithm that has been > employed since at least this discussion took place in 2002: > http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00359.html > In other words, refinement is not done on the basis of energy differences, > Ramachandran plot, interatomic clashes, or other problems with geometry that > could arise at each interpolation step. > > Is that correct? If so, is there a way to customize the refinement that's > done? > > I am using MacPyMOL version 1.7.6.2. > > Regards, > > Emily. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e _______________________________________________ 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
