# [phenixbb] rmsd: phenix vs refmac

Karolina Michalska dziuba at amu.edu.pl
Fri Jan 23 01:31:18 PST 2009

```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.
>