[Chimera-users] Tube representation picture of the eigenvector

Prasanna Venkatesh prasannavenkatesh1 at gmail.com
Wed May 29 05:39:25 PDT 2013

Thank you very much for your help Elaine and Tom.

Prasannavenkatesh Durai

Ph.D. student
Innate Immunity, Cell Signaling and Molecular Modeling Lab
Ajou university, South korea.
Mobile- +82-10-2336-1984
Office- +82-31-219-1749
e-mail: prasanna at ajou.ac.kr&  prasannavenkatesh1 at gmail.com
Website: http://ws.ajou.ac.kr/~schoi/

On Wed, May 29, 2013 at 2:28 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Tom,
> The ViewMotions webserver does basically what you describe, plus the
> initial superposition of the structures.  Although the sessions from that
> server show licorice ribbon (I believe), it might work to hide ribbon and
> show CA trace instead, if the user prefers a more angular appearance.
> As you said, it is technically possible to generate something similar in
> Chimera given two input structures, with morphing and writing out the
> trajectory and reading it back in as multiple structures. However, neither
> ViewMotions nor Chimera compute eigenvectors.  That's the main reason I
> suspected VMD.
> Elaine
> On May 28, 2013, at 10:17 AM, Tom Goddard <goddard at sonic.net> wrote:
> > Hi Elaine,
> >
> >  A close look at that figure reveals that it is 20 stick models showing
> CA-traces side by side giving it the appearance of a flat sheet.  The CA
> positions move in a straight line from initial to final position.  Not sure
> if morph conformations can produce those linear interpolations.  If it
> could, and the morph frames were written out as separate PDBs and read back
> in to allow displaying them all at the same time, and rainbow model used,
> it could be possible to make that figure.  Needs testing to know if this
> works.
> >
> >       Tom
> >
> >
> > On May 28, 2013, at 10:04 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> >> Hi Prasanna,
> >> Although Chimera is credited, I am skeptical that Chimera was really
> used to make this figure.  As far as I know it's not possible to make
> something exactly like that in Chimera.  Maybe they really used VMD.  You
> could try asking the authors of the paper about it.
> >>
> >> For others on the list, the figure in question is:
> >> <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2479573/figure/fig5/>
> >>
> >> The most similar thing I can think of is to use the ViewMotions Rainbow
> web server:
> >> <http://viewmotions.bc.edu/>
> >>
> >> It takes your two structures and outputs a whole series of intermediate
> interpolated structures with rainbow color-coding as a Chimera session.
>  You can open the session in Chimera and adjust the view (rotate, scale,
> etc.) to your liking before saving an image.  This server is relatively new
> (2013) and was not available in 2008 when the figure discussed above was
> published.  It simply shows the differences between the two structures.  It
> would not necessarily be an eigenvector unless your method of creating the
> structures specifically makes them different only along an eigenvector.
> >>
> >> The other possibility in Chimera is to show a tube with circular
> cross-section proportional to the CA-CA distance between the two structures
> when they are superimposed.  This is really a tube, round not flat, and not
> colored differently from side to side as in the figure and the ViewMotions
> result.  Also it is only shown on one structure ( you have to pick which
> one) and thus does not really show the exact location of the other
> structure. To make that type of figure, you would:
> >> (a) open the two structures in Chimera, superimpose them with "mm #0 #1
> show true" which would also give a window with sequence alignment
> >> (b) in the sequence window, there will be an RMSD histogram above the
> sequences.  For two structures, this RMSD is the same as the CA-CA distance.
> >> (c ) in main Chimera, menu, choose "Tools…. Structure Analysis… Render
> by Attribute" and in that dialog, choose attribute of "residues" named
> "mavRMSD", and use the "Worms" section.  You would just apply this to one
> structure and hide the other one. More details on using this tool:
> >> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render
> >
> >>
> >> This Chimera approach could be based on an ensemble of structures (such
> as from NMR) and mainly shows which areas are more or less conformationally
> variable.
> >>
> >> I hope this helps,
> >> Elaine
> >>
> >>
> >> On May 28, 2013, at 8:48 AM, Prasanna Venkatesh <
> prasannavenkatesh1 at gmail.com> wrote:
> >>
> >>> Dear Chimera users and supporters,
> >>>  I would like to generate a tube representation picture similar to one
> in the article (Figure 5 in "MD Simulations of Papillomavirus DNA-E2
> Protein Complexes Hints at a Protein Structural Code for DNA Deformation").
> Through Gromacs, I have average.pdb and extreme.pdb of my protein for the
> MD simulations. Please help me by providing the steps to make the picture.
> I asked the question earlier but not getting the similar picture with the
> answer provided. I don't know I asked it right the last time. Thank you in
> advance.
> >>> Regards,
> >>> Prasanna.
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