[phenixbb] phenix.pdbtools question

[Pavel Afonine]

Hi Simon,

there must be something weird in your file... Could you please send me it?

Pavel.

On 10/21/2008 3:01 AM, Simon Kolstoe wrote:
> Dear phenix list,
>
> I am wanting to model a poly-proline structure. I created the file in  
> PyMOL, saved it as a pdb, and then tried to regularize it with:
>
> phenix.pdbtools polypro.pdb --geometry_regularization
>
> However the program reported (snipped to the last few lines):
>
> ATOM     63  CD  PRO     6      -3.290   3.487  -2.968  1.00   
> 0.00           C
>        ATOM     69 2HD  PRO     6      -2.824   2.626  -3.453  1.00   
> 0.00           H
>      Distance model: 1.09209 (ideal: 0.97)
>        ATOM     63  CD  PRO     6      -3.290   3.487  -2.968  1.00   
> 0.00           C
>        ATOM     70 3HD  PRO     6      -4.165   3.171  -2.396  1.00   
> 0.00           H
>      Distance model: 1.44721 (ideal: 1.473)
>        ATOM     57  N   PRO     6      -2.321   4.145  -2.118  1.00   
> 0.00           N
>        ATOM     63  CD  PRO     6      -3.290   3.487  -2.968  1.00   
> 0.00           C
>      Distance model: 1.53855 (ideal: 1.525)
>        ATOM     58  CA  PRO     6      -1.810   5.407  -2.632  1.00   
> 0.00           C
>        ATOM     59  C   PRO     6      -2.332   6.603  -1.817  1.00   
> 0.00           C
>      Distance model: 1.23088 (ideal: 1.231)
>        ATOM     59  C   PRO     6      -2.332   6.603  -1.817  1.00   
> 0.00           C
>        ATOM     60  O   PRO     6      -3.080   6.424  -0.856  1.00   
> 0.00           O
> Sorry: Number of bonds with excessive lengths: 74
>
> I thought the whole purpose of geometry regularization was to get rid  
> of excessive lengths, not just tell me they are there!! How do I get  
> the program to really regularize my geometry?
>
> Thanks,
>
> Simon
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