[phenixbb] phenix.pdbtools question
Simon Kolstoe
s.kolstoe at ucl.ac.uk
Tue Oct 21 03:01:28 PDT 2008
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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