[Chimera-users] Fwd: Double coordinates for same residue

[Francesco Pietra]

Addendum: I am aware about "alternate positions", what I don't know is
how to treat such a protein, or whether it should be better to abandon
modeling it. I have no idea which alternate position should be better
deleted.
francesco pietra


---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Thu, Sep 15, 2011 at 5:31 PM
Subject: Double coordinates for same residue
To: chimera <chimera-users at cgl.ucsf.edu>


Hello:

Surely a naive question: While beginning to treat a multichain,
engineered protein - downloaded from PDB web (1.94 A resolution) -
with Chimera, I noticed that many amino acids have such feature as GLU
252 below. Same for many SER, ILE, HIS (two imidazole rings for the
same residue number)

ATOM   2022  N   GLU A 252      15.171 -45.532  45.115  1.00 26.12           N
ATOM   2023  CA AGLU A 252      14.023 -44.631  45.214  0.50 26.30           C
ATOM   2024  CA BGLU A 252      14.048 -44.592  45.252  0.50 26.30           C
ATOM   2025  C   GLU A 252      13.983 -43.654  44.050  1.00 25.90           C
ATOM   2026  O   GLU A 252      12.894 -43.403  43.470  1.00 25.36           O
ATOM   2027  CB AGLU A 252      13.974 -43.909  46.559  0.50 26.93           C
ATOM   2028  CB BGLU A 252      14.170 -43.759  46.533  0.50 26.77           C
ATOM   2029  CG AGLU A 252      13.283 -44.741  47.629  0.50 29.02           C
ATOM   2030  CG BGLU A 252      12.874 -43.673  47.313  0.50 29.14           C
ATOM   2031  CD AGLU A 252      14.088 -45.948  48.051  0.50 33.10           C
ATOM   2032  CD BGLU A 252      12.806 -44.716  48.426  0.50 31.91           C
ATOM   2033  OE1AGLU A 252      13.481 -47.014  48.330  0.50 34.82           O
ATOM   2034  OE1BGLU A 252      13.394 -44.454  49.504  0.50 31.18           O
ATOM   2035  OE2AGLU A 252      15.333 -45.828  48.101  0.50 35.49           O
ATOM   2036  OE2BGLU A 252      12.162 -45.782  48.231  0.50 33.14           O
ATOM   2037  N   GLU A 253      15.141 -43.133  43.683  1.00 24.58           N
ATOM   2038  CA  GLU A 253      15.225 -42.212  42.559  1.00 25.11           C
ATOM   2039  C   GLU A 253      14.838 -42.941  41.242  1.00 23.83           C
ATOM   2040  O   GLU A 253      14.142 -42.383  40.374  1.00 23.54           O
ATOM   2041  CB  GLU A 253      16.637 -41.603  42.476  1.00 26.18           C
ATOM   2042  CG  GLU A 253      17.033 -40.722  43.697  1.00 30.81           C
ATOM   2043  CD  GLU A 253      17.635 -41.491  44.915  1.00 36.16           C
ATOM   2044  OE1 GLU A 253      17.540 -42.742  45.032  1.00 35.80           O
ATOM   2045  OE2 GLU A 253      18.198 -40.809  45.801  1.00 40.87           O

About the protein:
SOURCE   2 ORGANISM_SCIENTIFIC: PSEUDOMONAS MENDOCINA;
SOURCE   3 ORGANISM_TAXID: 300;
SOURCE   4 GENE: TMOA;
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: P58KABE;

The said residue are not among those not located in the experiment.

I am interested in channels, pores and so on in the protein, so that
the above issue is of most concern for me.

Thanks for aid

francesco pietra