Now I see what you did. I tried exact same things myself using an arbitrary structure from PDB. I couldn't reproduce your problem using both: the current development code and the latest CCI Apps: 2008_02_08_1610. In this case I can only work on this problem if you send us the reproducer so we can reproduce your problem. Pavel. On 2/21/2008 6:06 PM, Jianghai Zhu wrote:
Sorry, I should have made it clear.
I started a refinement using phenix.refine with riding H in my model. After the refinement, I got the following at the end of the log and the header of the pdb file.
stage angl bond chir dihe plan repu geom_target 0 : 1.394 0.124 0.147 20.782 0.004 3.925 1.1922e+00 ... 6_bss: 0.622 0.011 0.120 13.143 0.003 3.822 2.6112e-02
Using this refined model, I did phenix.pdbtools model.pdb --show-geometry-statistics. And I got the following.
|-Geometry statistics---------------------------------------------------------| | Type | Count | Deviation from ideal | Targets | Target (sum) | | | | rmsd max min | | | | bond | 99522 | 0.004 0.085 0.000 | 0.028 | | | angle | 179035 | 0.793 21.106 0.000 | 0.099 | | | chirality | 7686 | 0.126 4.889 0.000 | 0.396 | 0.060 | | planarity | 15814 | 0.004 0.089 0.000 | 0.060 | | | dihedral | 24985 | 15.478 87.363 0.000 | 1.129 | | | nonbonded | 99522 | 3.939 4.900 1.125 | 0.725 | | |-----------------------------------------------------------------------------|
Using this refined model, I did phenix.refine model.pdb data.mtz main.number_of_macro_cycles=0 strategy=none. And I got the following.
------------------------------------------------------------------------ stage angl bond chir dihe plan repu geom_target 0 : 0.608 0.003 0.120 12.395 0.003 3.928 2.9651e-02 ------------------------------------------------------------------------
After removing the H from the refined model, I did phenix.pdbtools model_noH.pdb --show-geometry-statistics. And I got the following.
|-Geometry statistics---------------------------------------------------------| | Type | Count | Deviation from ideal | Targets | Target (sum) | | | | rmsd max min | | | | bond | 51167 | 0.005 0.085 0.000 | 0.054 | | | angle | 69163 | 1.030 21.106 0.000 | 0.194 | | | chirality | 7686 | 0.126 4.889 0.000 | 0.396 | 0.142 | | planarity | 9110 | 0.005 0.089 0.000 | 0.104 | | | dihedral | 18756 | 17.864 87.363 0.000 | 1.504 | | | nonbonded | 51167 | 4.092 4.900 1.434 | 0.639 | | |-----------------------------------------------------------------------------|
Jianghai
On Feb 21, 2008, at 8:35 PM, Pavel Afonine wrote:
Hi Jianghai,
I'm confused about what you're comparing with what. Could you please try this:
1) Take a model;
2) Run phenix.refine with it:
% phenix.refine model.pdb data.mtz main.number_of_macro_cycles=0 strategy=none
3) Run phenix.pdbtools with it:
% phenix.pdbtools model.pdb --show-geometry-statistics
Is the geometry statistics reported by phenix.refine and phenix.pdbtools different? If it is different then there is a problem and to fix it I will need to look at that PDB file.
Pavel.
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