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
Hi Bo,
On Tue, 04 Nov 2008 03:04:10 -0800 (PST), Bo Yang n62star@yahoo.com wrote:
> 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
I think the problem is just that modeller is not writing out the atom name correctly. In a proper PDB file, the element symbol should be right-justified in columns 13-14. So your line above should start with:
HETATM 3620 FE BLK 455 not HETATM 3620 FE BLK 455
If you edit the PDB files as output by modeller you can fix that. Otherwise, you need to select the Fe by atom name, rather than element in Chimera or VMD. I have seen the same problem when incorporating calcium ions in a structure.
Cheers, Rob
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Robert Campbell