[phenixbb] adding sutrates in phenix.refine
Maia Cherney
chern at ualberta.ca
Wed Aug 12 06:30:45 PDT 2009
Have you tried replacing ' with *?
Maia
Rune wederkinck Andersen wrote:
> Hi everyone
> I'm running a refinement in phenix.refine. I'm now trying to ad two
> subtrates AMP and RP5. The phenix.refine seams to reconise AMP but
> not the RP5 molecules. It seams as if this molecules is well known for
> the program
> (phenix-1.4-3/ext_ref_files/chemical_components/r/data_RP5.cif).
> In my PDB file the two molecules are described like this:
> ...
> HETATM 19 C6 AMP A 301 35.852 19.986 36.427 1.00 22.32 A
> HETATM 20 N6 AMP A 301 35.448 19.736 37.693 1.00 24.44 A
> HETATM 21 N7 AMP A 301 36.400 17.540 35.616 1.00 23.01 A
> HETATM 22 C8 AMP A 301 36.853 17.097 34.416 1.00 21.98 A
> HETATM 23 N9 AMP A 301 37.034 18.126 33.560 1.00 19.84 A
> HETATM 1 P' RP5 A 302 30.291 24.910 31.815 0.25 10.66 A
> HETATM 2 C5' RP5 A 302 32.348 25.416 30.301 0.25 14.76 A
> HETATM 3 O5' RP5 A 302 31.481 24.448 30.868 0.25 12.67 A
> HETATM 4 C4' RP5 A 302 33.260 24.753 29.307 0.25 15.58 A
> HETATM 5 C3' RP5 A 302 33.017 25.227 27.872 0.25 15.17 A
> HETATM 6 O3' RP5 A 302 33.951 26.264 27.522 0.25 14.15 A
> HETATM 7 C2' RP5 A 302 33.282 23.935 27.083 0.25 16.11 A
> HETATM 8 O2' RP5 A 302 34.571 23.963 26.478 0.25 13.68 A
> HETATM 9 C1' RP5 A 302 33.351 22.848 28.160 0.25 16.92 A
> HETATM 10 O1' RP5 A 302 32.775 23.415 29.296 0.25 16.62 A
> HETATM 11 O1 RP5 A 302 32.631 21.639 27.867 0.25 20.12 A
> HETATM 12 O1X RP5 A 302 29.112 25.373 30.809 0.25 10.53 A
> HETATM 13 O2X RP5 A 302 29.912 23.844 32.781 0.25 10.59 A
> HETATM 14 O3X RP5 A 302 30.793 26.258 32.567 0.25 9.63 A
> ATOM 1 N MET B 1 63.305 2.511 45.667 1.00 64.80 B
> ATOM 2 CA MET B 1 62.528 3.463 46.463 1.00 68.29 B
> ATOM 3 C MET B 1 62.555 4.863 45.882 1.00 65.73 B
> ATOM 4 O MET B 1 63.607 5.325 45.446 1.00 64.47 B
> ...
>
> I have tried with phenix.elbow as well but didn't work...
>
> Please help...
>
> Rune
>
>
>
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