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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