Dear All, I am having some trouble using the standalone HOLE script. I am trying to plot a very odd ion pathway but for some reason HOLE just won’t plot the most obvious route. I have tried extensively to play around with the CVECT and CPOINTs, which doesn’t seem to do the trick. Problem is there are quite a few paths and the largest (pore radius) path by visual inspection is not always selected. I can get it to work for some of the structures but not all.
I then decided to try alternatives and started using Coot’s implementation of HOLE. I also noticed there is already a older post on the forum by Oliver Clarke with a very similar question but I could not locate the answer to his question. Basically I was wondering if there is a way to output the HOLE plot in coot so that it can be visualized in Pymol or Chimera/ChimeraX. I am using Coot 0.9.6 EL on my windows machine at the moment. If this isn’t possible, can anyone suggest an alternative where I can specify the path more accurately? I have been placing water molecules and noting the coordinates as an input CPOINT in the hole.inp file, but the program seem to not follow this very accurately. PS I love the new coot 😊, thank you for all the hard work. Best, Omid --------------------------------------------------- --------------------------------------------------- Dr. Omid Haji-Ghassemi Assistant Professor, Biological Sciences Department University of Calgary https://hajighassemilab.org ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
