[phenixbb] phenix.pdbtools question

[James Fraser]

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
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>



-- 
James Fraser
jamesfraser at berkeley.edu
Alber Lab
356 Stanley Hall, QB3
UC Berkeley
Berkeley, CA 94720
http://ucxray.berkeley.edu/~jfraser/