[phenixbb] phenix.pdbtools question

[Simon Kolstoe]

Thanks for the tip.

A CRYST1 card solved the problem.

Simon


On 21 Oct 2008, at 16:08, James Fraser wrote:

> I've noticed this error too.  It occured when I was missing a CRYST 1
> line in my PDB.   I'm not sure if just any old CRYST 1 line will work,
> but if you generate one that has a very large P1 cell, your error
> should go away.
>
> jf
>
> On Tue, Oct 21, 2008 at 7:47 AM, Pavel Afonine <pafonine at lbl.gov>  
> wrote:
>> 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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>>> phenixbb at phenix-online.org
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>>>
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>
>
>
> -- 
> James Fraser
> jamesfraser at berkeley.edu
> Alber Lab
> 356 Stanley Hall, QB3
> UC Berkeley
> Berkeley, CA 94720
> http://ucxray.berkeley.edu/~jfraser/
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