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/measure.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/volumepathtracer/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@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/Scripts/dividelinks.p...) 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.