[Chimera-users] Visualize 3-10 helix

[Elaine Meng]

Hi Yangqi
Even though it is often included in the PDB file HELIX lines, Chimera does not automatically tag different kinds of helix.  They are all lumped together in “helix”

Although it is not very convenient, to find out which residues are in 3-10 helices in many deposited structures, you can look in the PDB file text for the HELIX lines, and then see the number in column 40 as described here (“1” is right-handed alpha, “5” is right-handed 3-10, etc.):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#secondary <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#secondary>>

For example, I see that 3KK4 has several 3-10 helices by looking in the text of its PDB file.  Looking at chain A only, the HELIX lines are:

HELIX    1   1 ASN A   -1  ARG A    7  1                                   9
HELIX    2   2 ASN A    9  TYR A   13  5                                   5
HELIX    3   3 GLN A   33  ASP A   46  1                                  14
HELIX    4   4 ARG A   49  GLY A   66  1                                  18
HELIX    5   5 ASN A   70  GLU A   88  1                                  19
HELIX    6   6 PRO A   98  LEU A  102  5                                   5
HELIX    7   7 ASP A  103  ARG A  109  1                                   7
HELIX    8   8 PRO A  112  TYR A  116  5                                   5

That means chain A residues 9-13, 98-102, and 112-116 were  identified as 3-10 helix.  

If you wanted to use that information, you could (for example) make an alias for that set of residues for convenience in later commands, or just specify them directly, say

open 3kk4
delete ~ :.a
alias tthel :9-13,98-102,112-116
color red tthel
sel tthel

(B) If you wanted to identify 3-10 helices directly from the structure (say it was just a model you built or some other undeposited structure), you could use the FindHBond tool or command and then identify where the mainchain H-bonds are i,i+3, and whether the conformation appears helical.  I don’t think it is obvious from the backbone angles whether it is alpha or 3-10 helix.   For example with 3kk4

select helix & @n,o
hbonds selRestrict both log true

…and then look in the Reply Log for i,i+3 backbone H-bonds.  For chain A I get:

H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GLU 3.A N    ASN -1.A O    no hydrogen  2.948  N/A
ILE 4.A N    ALA 0.A O     no hydrogen  2.993  N/A
PHE 5.A N    MSE 1.A O     no hydrogen  3.085  N/A
ILE 6.A N    CME 2.A O     no hydrogen  2.832  N/A
SER 12.A N   ASN 9.A O     no hydrogen  2.979  N/A
TYR 13.A N   GLN 10.A O    no hydrogen  3.327  N/A
LEU 34.A N   SER 12.A O    no hydrogen  2.914  N/A
ASP 37.A N   GLN 33.A O    no hydrogen  2.912  N/A
VAL 38.A N   LEU 34.A O    no hydrogen  2.904  N/A
[…]
GLU 88.A N   VAL 84.A O    no hydrogen  2.885  N/A
SER 101.A N  PRO 98.A O    no hydrogen  3.050  N/A
LEU 102.A N  ILE 99.A O    no hydrogen  2.968  N/A
VAL 107.A N  ASP 103.A O   no hydrogen  2.991  N/A
LEU 108.A N  ALA 104.A O   no hydrogen  3.010  N/A
ARG 109.A N  GLN 105.A O   no hydrogen  3.055  N/A
LEU 115.A N  PRO 112.A O   no hydrogen  3.035  N/A
53 hydrogen bonds found

… whereas if I just select the residues that the PDB file says are 3-10 

select tthel & @n,o
hbonds selRes both log t

I get:
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
SER 12.A N   ASN 9.A O    no hydrogen  2.979  N/A
SER 12.A N   ASN 9.A OD1  no hydrogen  3.067  N/A
SER 12.A OG  ASN 9.A O    no hydrogen  2.589  N/A
TYR 13.A N   GLN 10.A O   no hydrogen  3.327  N/A
SER 101.A N  PRO 98.A O   no hydrogen  3.050  N/A
LEU 102.A N  ILE 99.A O   no hydrogen  2.968  N/A
LEU 115.A N  PRO 112.A O  no hydrogen  3.035  N/A
7 hydrogen bonds found

(C) I don’t think you can tell 3-10 from other helix using just phi-psi angles, but to examine those angles you can show the protein Ramachandran Plot (Favorites… Model Panel, choose model on the left and then the Ramachandran plot button on the right).  Then when you select any residue(s) they will show up on the plot as red dots.    
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/ramachandran.html <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/ramachandran.html>>
Or, you can select any single residue and click the green magnifying glass on the lower right corner of the Chimera window to show the Selection Inspector, then in that dialog choose to Inspect: “Residue”  and it shows you the phi angle and psi angle values.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 15, 2018, at 11:47 AM, BuddySphinx <yangqi.gu at yale.edu> wrote:
> 
> Dear Chimera users,
> I am wondering if there is a quick way in Chimera to visualize 3-10 helix? Or showing the dihedral angle of the peptide bonds?
> Best,
> Yangqi

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