[Chimera-users] setting secondary structure of amino acid residues

Haresh Tukaram More htm211 at nyu.edu
Thu Jan 30 10:53:04 PST 2014

Hi Elaine,

I made two different models in a single Chimera window and selected the
N-terminal amino acid of one peptide and C-terminal amino acid of another.
Then I ran the command Join mdoels, but it gives me the error. Can you
please tell me what I am doing wrong here.

I have attached screen shot of the window.


On Tue, Jan 28, 2014 at 6:36 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Haresh,
> To run ksdssp, just enter command "ksdssp" ... this does not change the
> coordinates of the structure, it just tries to identify which parts are
> helix and which are strand based on where it sees backbone H-bonds. If the
> ribbon is still not like the helix or strand width after you use "ksdssp"
> it means that the conformation does not look like helix or strand according
> to ksdssp.
> When you use addaa, make sure to specify the desired conformation.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addaa.html>
> Another way instead of addaa to build the 14 residues is with Build
> Structure (in menu under Tools... Structure Editing), section Start
> Structure, choice "peptide", which will then give a further dialog for
> setting phi/psi angles with suggestions available for different secondary
> structures.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start
> >
> You would build the peptide as a separate new model, but then use the Join
> Models section of Build Structure to attach it to the N-term of your
> protein.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join
> >
> HOWEVER, even if you built the conformation correctly, it depends whether
> you tried to make a strand or a helix.  Even if the peptide is in a
> beta-strand conformation, ksdssp will not identify a single strand by
> itself.  It only identifies a beta-strand when the backbone is positioned
> to H-bond with another beta-strand, as in a hairpin or sheet.
> You could just force Chimera to show the residues as helix or strand no
> matter what the reality is or what ksdssp thinks, for example, selecting
> all those residues and then if you wanted them to be considered strand,
> using commands:
> setattr r isHelix false sel
> setattr r isStrand true sel
> (just trade "isHelix" and "isStrand" in those commands if you wanted the
> residues to be considered helix)
> For helix, an additional possibility is to try using ksdssp again but with
> command-line options to use less strict parameter values.  <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>
> You can search the manual for strings like "ksdssp" or "building peptides"
> from the Chimera Help menu.
> Best,
> 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 Jan 28, 2014, at 2:43 PM, Haresh Tukaram More <htm211 at nyu.edu> wrote:
> > Hi Elaine,
> > Yes I did exactly the way you explained and it is working now.
> > I have another question. I need to add some 14 residues on N-termius of
> the protein which I did using the addaa command. However, I am unable to
> simulate its secondary structure using ksdssp. I am not sure how to run
> this command in command line. Or am I doing something wrong in terms of
> predicting the structures.
> > Can you please let me know what do I need to do in terms of getting the
> structure of protein after addsing residues on N-terminus.
> > Thanks,
> > Haresh
> >
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