[phenixbb] phenix.pdbtools question
Simon Kolstoe
s.kolstoe at ucl.ac.uk
Tue Oct 21 08:21:45 PDT 2008
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
>>> _______________________________________________
>>> phenixbb mailing list
>>> 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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