Hi, Has anyone solved this problem? I am also fighting with extremly low rmsd values. For 1.7A structure I get rmsd 0.004A (bond) 0.733 (angles) (R/Rfree=0.1884/0.2216) with automatic weight calculation. When I want to loose restraints to get more reasonable rmsd I get R/Rfree 0.1814/0.2240). However, at the moment I do not know what "reasonable" means while using phenix.refine. Is seems to me that the program include hydrogen atoms in rmsd calculations. I have done a test and run pdbtools for my structure refined with automatically adjusted weight and given manually. Below are the statistics given for a model with and without hydrogen atoms: Automatic with H Geometry statistics---------------------------------------------------------| | Type | Count | Deviation from ideal | Targets | Target (sum) | | | | rmsd max min | | | | bond | 5464 | 0.004 0.033 0.000 | 0.029 | | | angle | 9954 | 0.734 6.777 0.000 | 0.092 | |-----------------------------------------------------------------------------| Automatic without H |-Geometry statistics---------------------------------------------------------| | Type | Count | Deviation from ideal | Targets | Target (sum) | | | | rmsd max min | | | | bond | 2764 | 0.006 0.036 0.000 | 0.060 | | | angle | 3763 | 1.003 6.777 0.001 | 0.196 | | User-provided, with H -Geometry statistics---------------------------------------------------------| | Type | Count | Deviation from ideal | Targets | Target (sum) | | | | rmsd max min | | | | bond | 5464 | 0.023 0.177 0.000 | 0.924 | | | angle | 9954 | 1.592 12.640 0.000 | 0.549 | | User-provided, without H |-Geometry statistics---------------------------------------------------------| | Type | Count | Deviation from ideal | Targets | Target (sum) | | | | rmsd max min | | | | bond | 2764 | 0.032 0.177 0.000 | 1.832 | | | angle | 3763 | 2.343 12.640 0.001 | 1.317 | | Clearly, phenix.refine includes H in calculation. So if I want to get statistics similar to refmac output (which do not include H) I have to test several weights and check statistics given by pdbtools after H removal. Am I right? Karolina Dnia 2008-12-16, wto o godzinie 02:21 +0000, Frank von Delft pisze:
Hi
I thought that a while ago, I read somewhere that rmsd(bonds) had not been calculated the same way in phenix as in refmac. I believe it was in connection with automated weights, and that rmsd(bonds) always much lower in phenix.
I understood too that this had been adjusted since to match refmac.
But we're still seeing some much lower rmsd(bond) from phenix: in particular, when we take a refmac model and plug it straight into phenix, the rmsd for cycle zero is already much lower than what it was at the end of refmac.
Could someone enlighten...? (Yup, latest version of phenix.)
Thanks! phx _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb