[Chimera-users] Double coordinates for same residue

[Francesco Pietra]

Hello Elaine;
My addendum was sent before I could read your mail. I wonder whether
you could  answer the addendum by suggesting to delete alternate
position or avoiding to carry out molecular mechanics with such
coordinates. I intended to proceed with REDUCE.

Thanks
francesco

On Thu, Sep 15, 2011 at 6:13 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Francesco,
> Those A and B are "alternate location" identifiers, and they are part of standard PDB format.  Now with higher-resolution structures, sometime more than one position can be identified in the density map, and this allows the depositors to report those multiple positions.
>
> These are described in the "Intro to PDB Format" in the Chimera tutorials
> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>
> .. as well as at the PDB website
> <http://www.wwpdb.org/documentation/format33/sect9.html#ATOM>
>
> In Chimera you can specify these on the command line as
> @[atoms].[altlocs]
> similar to the what we do for chains,
> :[residues].[chains]
>
> Examples:
>
> color red @.a
> - color all atoms with alternate location A red
>
> ~disp :42 at .b
> - undisplay alternate location B atoms in residue 42
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
> On Sep 15, 2011, at 8:31 AM, Francesco Pietra wrote:
>
>> 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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>
>