[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.
>
> Could someone enlighten...? (Yup, latest version of phenix.)
>
> Thanks!
> phx
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