[Chimera-users] Calculating distances in and between sheets

[Einav Tayeb-Fligelman]

Hi Elaine,

Thank you very much for your elaborated answer!
The thing is that I tried, as a reference, your method on a structure that
a collaborator of us already calculated everything using a few PyMol
scripts, and I get a totally different number (12.6 vs. 11.3 A). I am just
not sure what it more accurate.
If you don't mind to try your method on my structure maybe you could offer
me some specific tips for these kind of calculations (since I have to do it
on many similar structures now).
The PDBID is 5i55. If you go to the "unit cell" window and set the copy
number on the Y axis to an higher value (I used at least 4) then you should
get two "sheets" of alpha-helices. I am trying to calculate the distance
between those sheets and the problem is that the planes are really not
parallel.
I used for the calculation only the backbone atoms and omitted the flanking
residues, but I am not sure that this is the best way to go.

I would really appreciate your help on that.

Thank you,
Einav

On Mon, Feb 5, 2018 at 9:40 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> A minor limitation of my “measure distance” method of getting the closest
> distance between two plane objects is that it only uses the disc surface
> vertices.  (Each plane display is actually a triangulated surface.)
>
> It is very minor in my opinion, really only affecting planes that actually
> intersect or are very close together.  For example, the closest distance
> between two intersecting planes might be reported as a small nonzero number
> because the surface vertices don’t exactly coincide.  I couldn’t figure out
> a way to show the discs as mesh to reveal the locations of the vertices,
> but my test of intersecting discs gave just 0.22 angstroms.
>
> Elaine
>
> > On Jan 27, 2018, at 9:27 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Dear Einav,
> > There may not be a way to do exactly what you want, since for distance
> measurements the planes are treated as infinite.  However, axes are treated
> as finite line segments for distance measurements (although infinite for
> angle measurements), so I would have guessed it would work, but maybe not
> with the specific geometry of your system.
> >
> > One idea is that you can use command “measure distance” to report the
> minimum distance between one set of atoms and another, and in that case I'd
> use only CA atoms or N,CA,C,O to avoid the variability from sidechains.  I
> would do it several times (say for different regions of the sheets) to see
> the spread of the resulting values.
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/
> measure.html#distance>
> >
> > Oooh, I just thought of a trick: use this command to measure the minimum
> distance between the discs of defined planes (but treating them as finite)
> and to my surprise, it actually worked!!
> >
> > (1) define two planes
> > (2) Ctrl-click one to select it, command: namesel sel1
> > (3) Ctrl-click the other plane to select it, command: namesel sel2
> > (4) command: measure distance sel1 sel2
> >
> > (I thought it wouldn’t work because these plane surfaces are hidden from
> the model panel, but as far as I can tell, the distance reported in the
> status line and Reply Log is correct for my two planes)
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> >> On Jan 27, 2018, at 1:56 AM, Einav Tayeb-Fligelman <einavt at gmail.com>
> wrote:
> >>
> >> Dear all,
> >> I am trying to calculate distances in a unique structure in which
> alpha-helices stack into sheets, as in beta-sheets. I wish to calculate the
> distance between two facing sheets and between helices along each sheet.
> The structure theoretically contains tens of thousands of helices in each
> sheet (the content of the asymmetric unit is only one helix and the rest
> are a result of symmetry operations).
> >> I tried creating planes, one for each sheet, and calculate their
> distances, but I get zero since the planes are not exactly parallel.
> >> I also tried calculating centroid to centroid distance (I used 4
> helices for each sheet), but there is an angle between the centroids and
> therefore I get a longer value then expected. Same when calculating axis to
> axis distance.
> >> Is there a good way to calculate such things with chimera? and if so, I
> would appreciate an explanation for an "alpha-helical sheet" containing
> structure, as well as for facing beta-sheets containing structure (in case
> there is a difference in the explanation).
> >>
> >> Thank you in advance,
> >> Einav
> >>
> >>
> >> --
> >> PhD student at the Landau lab
> >> Faculty of Biology
> >> Technion, Israel Institute of Technology
> >> Haifa, Israel
> >> E-mail :einavtf at campus.technion.ac.il
> >> Tel at the lab:+972-77-8871964
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>


-- 
PhD student at the Landau lab
Faculty of Biology
Technion, Israel Institute of Technology
Haifa, Israel
E-mail :einavtf at campus.technion.ac.il
Tel at the lab:+972-77-8871964 <+972%2077-887-1964>
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