Hi Paul, Thank you so much for the quick reply. I am Be wonderful if this could get added to coot 1.0 also. I also have some additional questions/suggestions, though I am not sure how much time this will take to implement some of my suggestions.
1. I tried running the script, but I get an error: File "<string>", line 1, in <module> File "C:/Work/IpT/Cryosparc/HOLE/April_2022/Local/coot_hole.py", line 4, in <module> with open(fn) as f: IOError: [Errno 2] No such file or directory: 'hole-surface-dots.dat' I placed the 'hole-surface-dots.dat' in the project folder as well as the coot folder, but I get the same error? Do I need to modify the script to specify the location of the file? I tried the following: fn = "C:\XXX\hole-surface-dots.dat" but again I get the same error. 1. Would it be possible to add additional point to improve the “guidance” of the path? Perhaps as part of a script? Currently the path tends to take less obvious paths because only two points along the path can be specified, but I think this can easily be avoided if additional points can be specified. This is a problem in my case because I have a complicated ion permeation path which is not just a straight line. 1. Do I just need to cite coot and HOLE or also additional references for the HOLE implementation? 1. This is a nit picky one, but it would be great to clear the screen for all the previous HOLE plots so I don’t have to reload the pdb each time. Again this is probably more of a problem for me where I have to run the script multiple time until I get the optimal path. Probably not an issue for most. All the best, Omid From: Paul Emsley <pems...@mrc-lmb.cam.ac.uk> Sent: May 22, 2022 11:56 PM To: Omid Haji-Ghassemi <omid.hajighass...@ucalgary.ca>; COOT@JISCMAIL.AC.UK Subject: Re: HOLE pore radius in coot [△EXTERNAL] On 22/05/2022 21:09, Omid Haji-Ghassemi wrote: 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. Coot's HOLE has not been yet been ported/refactored/reworked for 1.0. Maybe your post will encourage me to bump it up the list... umm.. yes, I think it will! The column labels of hole-surface-dots.dat are: x y z r g b hexcol It is up to the rendering program to decide what shape to use for the points (a sphere seems reasonable) and what size the should be. Here's a script that renders the points in Coot 1.0 (it's quite slow because it works "atomically") - hopefully it will give you a start when reading it into PyMOL or ChimeraX. Paul. # ------------------ import coot fn = "hole-surface-dots.dat" with open(fn) as f: obj = coot.new_generic_object_number("HOLE Surface") lines = f.readlines() for line in lines: parts = line.split() x,y,z = [float(x) for x in parts[:3]] rgb = [float(x) for x in parts[3:6]] hexcol = parts coot.to_generic_object_add_point(obj, hexcol, 11, x, y, z) coot.set_display_generic_object(obj, 1) ######################################################################## 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/