Hi all,
I'm trying to use PyMol to add hydrogen atoms to this small fragment of
a PDB file, the chromophore from the GFP structure 1EMA;
REMARK S65T Chromophore from Ormo's coordintes (1EMB).
HETATM 466 N1 CRO 66 24.077 27.513 36.610 1.00
11.86 N
HETATM 467 CA1 CRO 66 25.011 26.478 37.078 1.00
7.34 C
HETATM 468 CB1 CRO 66 25.931 26.035 35.930 1.00
10.77 C
HETATM 469 CG1 CRO 66 25.155 25.422 34.796 1.00
16.67 C
HETATM 470 OG1 CRO 66 26.679 27.129 35.461 1.00
14.22 O
HETATM 471 C1 CRO 66 25.730 27.106 38.245 1.00
18.38 C
HETATM 472 N2 CRO 66 26.975 27.732 38.216 1.00
9.21 N
HETATM 473 N3 CRO 66 25.274 27.124 39.509 1.00
17.10 N
HETATM 474 C2 CRO 66 26.043 27.875 40.370 1.00
5.46 C
HETATM 475 O2 CRO 66 26.022 27.962 41.566 1.00
13.20 O
HETATM 476 CA2 CRO 66 27.197 28.245 39.512 1.00
16.08 C
HETATM 477 CA3 CRO 66 23.919 26.721 39.842 1.00
10.87 C
HETATM 478 C3 CRO 66 23.745 25.326 40.360 1.00
19.28 C
HETATM 479 O3 CRO 66 22.885 25.116 41.193 1.00
15.72 O
HETATM 480 CB2 CRO 66 28.329 28.822 39.960 1.00
10.75 C
HETATM 481 CG2 CRO 66 29.437 29.370 39.124 1.00
7.67 C
HETATM 482 CD1 CRO 66 29.541 29.103 37.742 1.00
11.31 C
HETATM 483 CD2 CRO 66 30.487 30.110 39.805 1.00
10.79 C
HETATM 484 CE1 CRO 66 30.707 29.546 37.033 1.00
17.44 C
HETATM 485 CE2 CRO 66 31.614 30.563 39.085 1.00
10.01 C
HETATM 486 CZ CRO 66 31.718 30.300 37.721 1.00
9.48 C
HETATM 487 OH CRO 66 32.894 30.804 36.971 1.00
13.84 O
CONECT 466 457 467
CONECT 467 466 468 471
CONECT 468 467 469 470
CONECT 469 468
CONECT 470 468
CONECT 471 467 472 473
CONECT 472 471 476
CONECT 473 471 474 477
CONECT 474 473 475 476
CONECT 475 474
CONECT 476 472 474 480
CONECT 477 473 478
CONECT 478 477 479 488
CONECT 479 478
CONECT 480 476 481
CONECT 481 480 482 483
CONECT 482 481 484
CONECT 483 481 485
CONECT 484 482 486
CONECT 485 483 486
CONECT 486 484 485 487
CONECT 487 486
END
Unfortunately, PyMol adds too many hydrogens to each carbon in the
tyrosine ring in the center of the chromophore. It doesn't recognize
that some of the carbons can have double bonds.
Does anyone know the best way to get PyMol to recognize the double bonds?
All the best,
--Buz
|---------------------------------------------------------|
Buz Barstow
192 Clark Hall
Cornell University
Ithaca, NY 14853, USA
Email: b...@cornell.edu
Phone: 607 255 8678
Fax: 607 255 8751
|---------------------------------------------------------|
