Hi John John Kuszewski wrote: > Hi L?on, > > On Mar 23, 2007, at 12:32 PM, L?on Salgado wrote: > >> >> I did tried to run an anneal.py with and without RAMA. And the results >> clearly show that the X best structures from the annealing with RAMA do >> show a better agreement (rmsd from superposition) between the mainchain >> as well as the sidechains on the ensemble. Great! > > You mean you've increased your protein structure's precision? That's > unusual. The > DELPHIC torsion angle potential (what I, too late, decided to call the > RAMA potential) > has minima corresponding to every observed combination of torsion > angles in the > database of xray structures it was built from. Thus, an unconstrained > sidechain won't > drop into a single conformation with refinement against the DELPHIC > torsions--it'll drop > into several conformations. The ensemble will be less of a continuous > smear of structures > at small scales (say, a single torsion angle), but it generally won't > look terribly different when > considering a protein structure as a whole. > > That said, the DELPHIC torsion potential clearly results in more > physically-reasonable > structures, and Ad Bax showed several years ago that it results in > better agreement with > observed RDCs in the absence of direct refinement against those RDCs. > So there's no > question that DELPHIC torsions improve the accuracy of protein > structures. But it's still > rare to see any significant change in their precision. >
My fault, I didn?t express myself correctly. Indeed, the residue sidechains of the generated structures with/without rama, do show an ensemble of configurations, but that's more clearly seen on the structures without rama. For example the rsmd for all heavy atoms from the mean struct., is 1.59/1.74 Angst, for structures generated with/without rama respectively, while the rmsd for the core backbone is aprox. 0.20/0.27. So, there's not a "significant change in their precision". >> >> But I still have one question, about the rama stuff. When I was reading >> and trying to understand some scripts using rama >> (eg.eginputs/sry/sry_finall.inp), I saw that the torsional database has >> 3 sets of potentials: the raw (called with xrama), gaussians (called >> with rama) and quartics (also called by rama). > > Just to fill in the background for others: The initial implementation > of the RAMA term would > read in a grid of potential values at a fixed (usually 2-5 degrees) > resolution. But it had fairly > rough atomic forces, and used a lot of memory. So I changed the > implementation to read > in fitted curves (either using Gaussian or quartic functions) > generated from the raw potential > grids. These are much less memory intensive and much smoother (and > therefore easier to > optimize). > >> When I call rama from >> python, what set am I using: gaussians or quartic? And am I using short >> range (intra-residue) as well as long range (inter-residues) >> correlations? > > Look at the code in xplor/python/protocol.py, starting around line > 570. It uses the 2D and 3D > potentials corresponding to intraresidue correlations only, fitted > with quartic functions. > > Ok. > >> One more. Reading the article [J. Magn. Res. 146, 249-254 (2000)], the >> authors define the DELPHIC torsions database as the original >> implementation of the torsion angle potential. So, when talking about >> the DELPHIC database, are we talking about the raw potentials or >> something else? > > I intended the term 'DELPHIC torsions' to apply to all implementations > of the method, > whether they use the raw grids, or fitted curves. The name 'RAMA' > came about because > it was initially just for backbone phi/psi angles. Unfortunately, it > became widely used > before I thought of the much snappier 'DELPHIC' name. Sigh. > [... snip ...] > Can I ask why you want to use the XRAMA implementation, anyway? > Now its more clear to me. I directly assigned the term DELPHIC, only to the raw potentials, not including the fitted curve potentials. Reporting again to http://nmr.cit.nih.gov/pipermail/xplor-nih/2004-March/000161.html , I was trying to understand what you meant by stating that "For peptides, it is probably reasonable to use the DELPHIC torsion potential for structures calculated in non-aqueous solvents." Many thanks, Cheers, L?on
