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[6]
        coot.to_generic_object_add_point(obj, hexcol, 11, x, y, z)
coot.set_display_generic_object(obj, 1)


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