Hello, I just tried this: - saved the ATOM/ANISOU lines provided below into a file zz.pdb - and then ran the command: phenix.pdb_atom_selection zz.pdb "name OD2 and altid A and chain B and resname ASP and resseq 271" which supposed to select the atom with the above selection string, and so it did it: (...) name OD2 and altid A and chain B and resname ASP and resseq 271 1 atom selected ATOM 6107 OD2AASP B 271 -19.758 19.638 48.708 0.50156.92 O (...) So, I'm not sure I understand what's happening. Can you make sure you are using the correct PDB file in phenix.refine run? There must be something obvious like this. If nothing helps, you can send me the full PDB file and phenix.refine command you used so I can reproduce this problem (I don't need data file - I can fake it). Pavel.

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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb