[Chimera-users] Visualize 3-10 helix

Mon Oct 15 14:15:42 PDT 2018

Hi Elaine,
Thank you for such a detailed answer! I am actually just checking the model
we built (undeposited). Some helices we built look like a 3-10 helices,
that's why I am interested. I will definitely try your suggestions!
Best,
Yangqi

On Monday, October 15, 2018, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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>
>
> 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>
> 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>
>
> 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
>
>
>

-- 

Yangqi Gu
Graduate Student
Malvankar Lab
Yale University, West Campus
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