Well, that is a more philosophical question that you will have to decide for yourself. There are also occupancy values (the column after the coordinates). In many cases it is reasonable to just delete the alternate positions with the lower occupancies. In your example A and B are equally strong (both 0.50), so one possibility is to just use one set and delete the others. For example, to delete all alternate locations B: delete @.b Another possibility is to make multiple models using the different locations. A structure with alternate locations may often be quite high resolution and high quality, so my personal opinion is you wouldn't want to throw the whole structure away just because you aren't sure what to do with these data. Elaine On Sep 15, 2011, at 9:14 AM, Francesco Pietra wrote:
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@gmail.com> Date: Thu, Sep 15, 2011 at 5:31 PM Subject: Double coordinates for same residue To: chimera <chimera-users@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
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