[Chimera-users] Addh function and fake N, C-terminii

[Elaine Meng]

Hi Gaëlle,
Chimera simply looks in the SEQRES lines of the PDB file to see the entire sequence of each chain.  Often, the atomic coordinates do not include all of these residues because they were not visible in the density map even though they were actually present in the crystallization experiment.

You can confirm this for yourself by looking at the PDB file in a text-editor, or in Chimera using the Sequence tool to show the extracted sequences (menu: Favorites… Sequence).  If you show the sequences for all 4 chains of 3L4F, you can see there are residues in the sequence that are not in the 3D solved structures; they are outlined with red outline boxes.  I attach an image of the Sequence window for chain D of this protein.  If you click into the sequence window (the real one, not this image of course) and put the mouse cursor over the sequence, it will report the structure residue number at the bottom of the window, or “no corresponding structure residue” for the ones that are missing from the 3D structure.

You can see in the image that the chain D protein in the experiment started with M634 (Met) even though its first structure residue is G652, and ended with an Ala even though its last structure residue R758.

If you only want to use the structure residues and not the SEQRES information to specify termini, you would text-edit to delete the SEQRES lines from the PDB file before opening it.

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 Jul 30, 2015, at 6:42 AM, gaelle garet <gaelle.garet at gmail.com> wrote:

> Hi, 
> I want to use Addh function to add hydrogens and protonate N, C-terminii but I don't understand very well how you detect if a terminus is fake or not.
> 
> For example, for the structure 3L4F, I obtain the following log : 
> 
> Chain-initial residues that are actual N terminii: MET 586.A, MET 586.B, MET 586.C
> Chain-initial residues that are not actual N terminii: GLY 652.D
> Chain-final residues that are actual C terminii: LEU 646.A, LEU 646.B
> Chain-final residues that are not actual C terminii: ASP 638.C, ARG 758.D
> 
> I don't understand why GLY 652.D, ASP638.C and ARG 758.D are not terminii,  can you explain me why and how the algorithm detect that ?
> Thank you in advance for your answer.
> -- 
> Gaëlle

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