[phenixbb] a double conformation residue included in metal coordination file
Yamei Yu
ymyuxtal at gmail.com
Tue Jun 7 07:57:30 PDT 2011
HI all,
In my structure, there is a double conformation residue and on
conformation is coordinated to a metal.
I use phenix.metal_coordination to generate a elbow.edits file. In
such file the restraint listed as:
refinement.geometry_restraints.edits {
bond {
action = *add
atom_selection_1 = name MG and chain B and resname MG and resseq 2001
atom_selection_2 = name OD2 and altid A and chain B and resname
ASP and resseq 271
distance_ideal = 2.070000
sigma = 0.100
}
}
But when I use this file for refinement, I got an error message:
Sorry: No atom selected: "name OD2 and altid A and chain B and resname
ASP and resseq 271"
I also check my PDB file:
ATOM 6100 N AASP B 271 -19.420 19.064 51.907 0.50115.36 N
ANISOU 6100 N AASP B 271 14002 14643 15186 -598 738 -1235 N
ATOM 6101 CA AASP B 271 -18.016 18.977 51.528 0.50127.08 C
ANISOU 6101 CA AASP B 271 15508 16123 16656 -585 725 -1202 C
ATOM 6102 C AASP B 271 -17.194 19.859 52.460 0.50105.81 C
ANISOU 6102 C AASP B 271 12832 13418 13952 -583 730 -1182 C
ATOM 6103 O AASP B 271 -17.750 20.593 53.277 0.50 67.89 O
ANISOU 6103 O AASP B 271 8027 8614 9153 -586 738 -1193 O
ATOM 6104 CB AASP B 271 -17.818 19.429 50.080 0.50154.71 C
ANISOU 6104 CB AASP B 271 18986 19641 20157 -560 689 -1204 C
ATOM 6105 CG AASP B 271 -18.871 18.868 49.141 0.50167.83 C
ANISOU 6105 CG AASP B 271 20622 21317 21830 -559 682 -1230 C
ATOM 6106 OD1AASP B 271 -18.804 17.661 48.823 0.50157.05 O
ANISOU 6106 OD1AASP B 271 19265 19945 20462 -568 691 -1224 O
ATOM 6107 OD2AASP B 271 -19.758 19.638 48.708 0.50156.92 O
ANISOU 6107 OD2AASP B 271 19211 19952 20460 -550 666 -1256 O
ATOM 6108 N BASP B 271 -19.303 18.972 52.212 0.50115.36 N
ANISOU 6108 N BASP B 271 14002 14643 15186 -598 738 -1235 N
ATOM 6109 CA BASP B 271 -17.822 18.681 52.128 0.50127.08 C
ANISOU 6109 CA BASP B 271 15508 16123 16656 -585 725 -1202 C
ATOM 6110 C BASP B 271 -17.006 19.773 52.851 0.50105.81 C
ANISOU 6110 C BASP B 271 12832 13418 13952 -583 730 -1182 C
ATOM 6111 O BASP B 271 -17.610 20.704 53.419 0.50 67.89 O
ANISOU 6111 O BASP B 271 8027 8614 9153 -586 738 -1193 O
ATOM 6112 CB BASP B 271 -17.514 18.729 50.592 0.50154.71 C
ANISOU 6112 CB BASP B 271 18986 19641 20157 -560 689 -1204 C
ATOM 6113 CG BASP B 271 -16.455 17.692 50.152 0.50167.83 C
ANISOU 6113 CG BASP B 271 20622 21317 21830 -559 682 -1230 C
ATOM 6114 OD1BASP B 271 -16.846 16.720 49.601 0.50157.05 O
ANISOU 6114 OD1BASP B 271 19265 19945 20462 -568 691 -1224 O
ATOM 6115 OD2BASP B 271 -15.310 17.950 50.520 0.50156.92 O
ANISOU 6115 OD2BASP B 271 19211 19952 20460 -550 666 -1256 O
Is there something wrong?
Thank you very much!
yamei yu
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