[ccp4bb] PHASER packing function with DNA

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Zinc or Iron binding protein, that is a question!
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2009-08-06

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Subject: Re: PHASER packing function with DNA
From: LEDU Marie-Helene 161111 Marie-Helene {- dot -} LEDU {- at -} CEA {- dot -} FR
Date: 2009-08-06

Subject: PHASER packing function with DNA
From: LEDU Marie-Helene 161111 Marie-Helene {- dot -} LEDU {- at -} CEA {- dot -} FR
Date: 2009-08-06

Dear CCP4BBer,

I'm using Phaser 2.1.4 to solve a structure containing both protein and DNA.
The packing function works find with the protein, but does not recognize the
trace of the DNA. Does anyone know precisely what should be the pdb format ?
Here is the format that I'am using :
ATOM 1 P Gd C 1 23.560 11.045 11.025 1.00 53.18
P
ATOM 2 OP1 Gd C 1 24.884 10.499 11.417 1.00 54.98
O
ATOM 3 OP2 Gd C 1 22.319 10.778 11.791 1.00 44.44
O
ATOM 4 O5' Gd C 1 23.716 12.601 10.891 1.00 47.89
O
ATOM 5 C5' Gd C 1 24.689 13.001 9.945 1.00 42.99
C
ATOM 6 C4' Gd C 1 24.395 14.391 9.437 1.00 39.27
C
ATOM 7 O4' Gd C 1 23.172 14.464 8.683 1.00 35.25
O
ATOM 8 C3' Gd C 1 24.264 15.347 10.617 1.00 36.72
C
ATOM 9 O3' Gd C 1 25.063 16.487 10.335 1.00 34.52
O
ATOM 10 C2' Gd C 1 22.807 15.691 10.507 1.00 34.06
C
ATOM 11 C1' Gd C 1 22.474 15.641 9.080 1.00 27.89
C
ATOM 12 N9 Gd C 1 21.218 15.303 8.921 1.00 20.00
N
ATOM 13 C8 Gd C 1 20.436 14.344 9.523 1.00 20.00
C
ATOM 14 N7 Gd C 1 19.207 14.292 9.056 1.00 20.00
N
ATOM 15 C5 Gd C 1 19.159 15.275 8.076 1.00 20.00
C
ATOM 16 C4 Gd C 1 20.381 15.912 7.978 1.00 20.00
C
ATOM 17 N1 Gd C 1 18.457 16.733 6.390 1.00 20.00
N
ATOM 18 C2 Gd C 1 19.700 17.306 6.353 1.00 20.00
C
ATOM 19 N3 Gd C 1 20.705 16.934 7.129 1.00 20.00
N
ATOM 20 C6 Gd C 1 18.087 15.691 7.242 1.00 20.00
C
ATOM 21 O6 Gd C 1 16.928 15.244 7.199 1.00 20.00
O
ATOM 22 N2 Gd C 1 19.883 18.288 5.476 1.00 20.00
N

Thanks,

Marie-Ln

Laboratoire de Biologie Structurale et Radiobiologie
CEA/DSV/IBiTec-S/SB2SM
bat144, pièce 25
91191 Gif-Sur-Yvette
Tel : 33 (0)1 69 08 71 35
E-mail : marie-helene.ledu@cea.fr
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Next message:
Subject: Re: PHASER packing function with DNA
From: LEDU Marie-Helene 161111 Marie-Helene {- dot -} LEDU {- at -} CEA {- dot -} FR
Date: 2009-08-06