Hi, Rubben: I use dot (.) . Heme is shown as BLK in the model. Using Chimera and VMD, the whole molecule of heme is there, but not Fe. If I select "Fe" from "element", no selection returns. The "Fe" is in the pdb file as shown below: HETATM 3620  FE  BLK   455     -54.160  -1.094 -33.073  1.00999.99       1SG3621 HETATM 3621  CHA BLK   455     -55.567  -1.736 -30.032  1.00999.99       1SG3622 HETATM 3622  CHB BLK   455     -53.632  -4.396 -33.562  1.00999.99       1SG3623 HETATM 3623  CHC BLK   455     -53.011  -0.451 -36.189  1.00999.99       1SG3624 HETATM 3624  CHD BLK   455     -54.469   2.229 -32.529  1.00999.99       1SG3625 HETATM 3625  NA  BLK   455     -54.569  -2.714 -32.020  1.00999.99       1SG3626 HETATM 3626  C1A BLK   455     -55.107  -2.789 -30.763  1.00999.99       1SG3627 HETATM 3627  C2A BLK   455     -55.133  -4.176 -30.354  1.00999.99       1SG3628 HETATM 3628  C3A BLK   455     -54.608  -4.886 -31.328  1.00999.99       1SG3629 HETATM 3629  C4A BLK   455     -54.246  -3.991 -32.395  1.00999.99       1SG3630 HETATM 3630  CMA BLK   455     -54.416  -6.422 -31.313  1.00999.99       1SG3631 HETATM 3631  CAA BLK   455     -55.621  -4.804 -29.030  1.00999.99       1SG3632 HETATM 3632  CBA BLK   455     -56.992  -4.376 -28.593  1.00999.99       1SG3633 HETATM 3633  CGA BLK   455     -57.255  -5.010 -27.253  1.00999.99       1SG3634 HETATM 3634  O1A BLK   455     -56.915  -4.439 -26.202  1.00999.99       1SG3635 HETATM 3635  O2A BLK   455     -57.828  -6.104 -27.233  1.00999.99       1SG3636 HETATM 3636  NB  BLK   455     -53.437  -2.204 -34.573  1.00999.99       1SG3637 HETATM 3637  C1B BLK   455     -53.311  -3.583 -34.605  1.00999.99       1SG3638 HETATM 3638  C2B BLK   455     -52.782  -3.991 -35.882  1.00999.99       1SG3639 HETATM 3639  C3B BLK   455     -52.616  -2.872 -36.580  1.00999.99       1SG3640 HETATM 3640  C4B BLK   455     -53.040  -1.749 -35.784  1.00999.99       1SG3641 HETATM 3641  CMB BLK   455     -52.468  -5.428 -36.363  1.00999.99       1SG3642 HETATM 3642  CAB BLK   455     -52.091  -2.736 -38.019  1.00999.99       1SG3643 HETATM 3643  CBB BLK   455     -51.725  -3.825 -38.678  1.00999.99       1SG3644 HETATM 3644  NC  BLK   455     -53.752   0.535 -34.116  1.00999.99       1SG3645 HETATM 3645  C1C BLK   455     -53.394   0.607 -35.442  1.00999.99       1SG3646 HETATM 3646  C2C BLK   455     -53.466   1.977 -35.904  1.00999.99       1SG3647 HETATM 3647  C3C BLK   455     -53.869   2.676 -34.858  1.00999.99       1SG3648 HETATM 3648  C4C BLK   455     -54.062   1.807 -33.747  1.00999.99       1SG3649 HETATM 3649  CMC BLK   455     -53.156   2.502 -37.344  1.00999.99       1SG3650 HETATM 3650  CAC BLK   455     -54.149   4.182 -34.765  1.00999.99       1SG3651 HETATM 3651  CBC BLK   455     -53.972   4.970 -35.805  1.00999.99       1SG3652 HETATM 3652  ND  BLK   455     -54.923   0.052 -31.560  1.00999.99       1SG3653 HETATM 3653  C1D BLK   455     -54.874   1.432 -31.525  1.00999.99       1SG3654 HETATM 3654  C2D BLK   455     -55.330   1.916 -30.258  1.00999.99       1SG3655 HETATM 3655  C3D BLK   455     -55.681   0.681 -29.488  1.00999.99       1SG3656 HETATM 3656  C4D BLK   455     -55.392  -0.425 -30.350  1.00999.99       1SG3657 HETATM 3657  CMD BLK   455     -55.447   3.379 -29.780  1.00999.99       1SG3658 HETATM 3658  CAD BLK   455     -56.248   0.648 -28.080  1.00999.99       1SG3659 HETATM 3659  CBD BLK   455     -57.738   0.802 -28.197  1.00999.99       1SG3660 HETATM 3660  CGD BLK   455     -58.352   0.774 -26.836  1.00999.99       1SG3661 HETATM 3661  O1D BLK   455     -59.545   1.081 -26.729  1.00999.99       1SG3662 HETATM 3662  O2D BLK   455     -57.669   0.458 -25.858  1.00999.99       1SG3663 Thank you for your advice. Bo --- On Tue, 11/4/08, Rubben Torella <rubben.torella@gmail.com> wrote: From: Rubben Torella <rubben.torella@gmail.com> Subject: Heme To: n62star@yahoo.com Date: Tuesday, November 4, 2008, 1:01 AM Hi,Bo! What do you use in the alignment for heme? dot (.) or (*)? Because if you use (.), heme is considered as a block, while (*) consider heme as a co-factor. But you see heme and you can't see iron, or you can't see anything? I'm sorry if I don't understand your question. Rubben Torella