[Chimera-users] Does anyone know how to specify a "MarkerSet Link" to be used for findClash

Jun Ha Song junhasong at berkeley.edu
Sat Jul 8 17:34:35 PDT 2017

Dear Elaine,

I have been using *measure distance* a lot to get the  exact distance
between the markers of my interest, and cannot praise the function enough.

However, what exactly I am trying to search is whether there exist a
model-model gap of specific distance that I can specify in Å..

I am currently working on a project where I placed a cylindrical model
(which I open by opening a script that includes two markers to be the both
ends of the filament (or simply put, marker-marker distance = actin
filament length), and a Link, shown with radius of Actin filament to depict
the space Actin filament would actually occupy in 3D space.

And, knowing that various form of Actin-Acrin Cross-Linking Proteins have
very well defined and unique lengths, I wanted to just locate and visualize
any and all region(s) of my active models (=which are solely actin
filaments) that are spaced "exactly by cross-linking protein's length away
from each other". Then I would be able to pin-point presence of, and
location of, and potentially number of any cross-linking protein that is

And for Tom's script; I think it actually places *n* number of additional
markers along the Link (or Bond) that I have selected, where additional
markers share identical model ID as the model ID of the Link. Just
discovered that the script doesn't work simply by selecting two end
markers, but only by selecting a Link.

[image: Inline image 1]

And here is the exact task I was asking about. Of course. this time, I
placed markers on links to have some atoms to calculate distance with.

When I use the command of

*findclash sel test self overlapCutoff -90 hbondAllowance 0 bondSeparation

while selecting all new markers, I can visualize...

[image: Inline image 1]

something like this!

On Sat, Jul 8, 2017 at 4:47 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Jun Ha Song,
> Yes, links are just like bonds, and exist just in terms of connecting
> those endpoints, so you have to fill them in with atoms/markers for
> findclash to use.
> Q1: sorry, there is no way to specify just bonds in the command line, and
> even if you did, they wouldn’t be the XYZ-points needed by computations
> like findclash.  There is “bondzone” to make various zoning tools use
> points along bonds, but as far as I know it doesn’t affect distance
> measurements.  You could try it to make sure:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bondzone.html>
> Q2: there is “distance” to report just the distance between two specified
> atoms/markers and “measure distance” to find just the closest distance
> between 2 sets of atoms and/or surface vertices… are either of those useful
> in your case?
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meas
> ure.html#distance>
> For command-line specification, you can use model number and/or residue
> number (which is apparently the marker ID). When I create a marker file
> (attached below, test.cmm) from the example given in the Volume Tracer
> manpage,
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/v
> olumepathtracer/volumepathtracer.html#markerfiles>
> … one marker is residue 1 and the other is residue 2, but they don’t
> appear to have atom names.  So if the marker set is #0, I can use
> sel #0:1
> sel #0:2
> distance #0:1,2
> I don’t know how Tom’s script adds the markers along links (whether
> they’re in the same model as the original marker set, what residue numbers,
> etc.)
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Jul 8, 2017, at 2:41 PM, Jun Ha Song <junhasong at berkeley.edu> wrote:
> >
> > Hello,
> >
> > I want to search whether my models are close enough to be exactly apart
> from each other by the distance I specify.
> >
> > findClash appear to be tailor-made for the exact task I was hoping to
> do, but unfortunately, it appear to only search nearby atoms, not the
> links, even if I select the entire model which has both markers and links
> incorporated as its component.
> >
> > The only way that I can make my entire MarkerSet to be competent for
> findClash was to use Tom's dividelinks.py script (
> http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scri
> pts/dividelinks.py) to add n number of marker s along the link of two
> marker that I selected.
> >
> > Q1. Can I ever specify MarkerSet Link by atom-spec commands, to use
> findClash on the inter-model links as well, not only for the markers?
> >
> > Q2. Is there any other function than findClash that allow me to find any
> inter-model (never atoms within the same model) atom or link's distance
> that I specify exist?
> >
> > Best,
> > Jun Ha Song.
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