Re: [COOT] HOLE pore radius in coot
Hi Paul, Thanks for the clarification. I didn’t even know about the generic object option, but now I know. I also figured out the error which results in the script not working. The output file is 'hole_surface_dots.dat' but the script is asking for 'hole-surface-dots.dat'. Don’t know how I missed that. It works fine now. My python scripting knowledge is quite poor. If it is not too much to ask would it be possible to lend me an example of a HOLE run script with more than two points are specified so I can adapt it to my example? All the best, Omid From: Mailing list for users of COOT Crystallographic Software On Behalf Of Paul Emsley Sent: May 25, 2022 4:35 PM To: COOT@JISCMAIL.AC.UK Subject: Re: HOLE pore radius in coot [△EXTERNAL] On 24/05/2022 15:52, Omid Haji-Ghassemi wrote: 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 "", line 1, in File "C:/Work/IpT/Cryosparc/HOLE/April_2022/Local/coot_hole.py", line 4, in with open(fn) as f: IOError: [Errno 2] No such file or directory: 'hole-surface-dots.dat' The script represents hole-surface-dots.dat. You need to have created that file first. 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. the filename (fn) needs to be in the current working directory - often that is the directory from which you started coot. 1. Would it be possible to add additional point to improve the “guidance” of the path? Yes, it's possible. 1. Perhaps as part of a script? All of Coot's HOLE functions are scriptable. 1. Currently the path tends to take less obvious paths because only two points along the path can be specified, It might be that - or it might be a bug. Or maybe the step size is too big. 1. 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. indeed - from the figure that I attached, you can see that the algorithm is supposed to handle paths that are not straight lines. 1. 1. Do I just need to cite coot and HOLE or also additional references for the HOLE implementation? Coot and HOLE would be fine. I don't think that I wrote it up formally (probably because it was largely (just) an implementation of Oliver's paper). I'd like it to carve out the path from a map and add arbitrary map caps - that might be worth a mention. 1. 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. Isn't this just a matter of undisplaying or closing the previous generic objects? Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=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/
Re: [COOT] HOLE pore radius in coot
On 24/05/2022 15:52, Omid Haji-Ghassemi wrote: 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 "", line 1, in File "C:/Work/IpT/Cryosparc/HOLE/April_2022/Local/coot_hole.py", line 4, in with open(fn) as f: IOError: [Errno 2] No such file or directory: 'hole-surface-dots.dat' The script represents hole-surface-dots.dat. You need to have created that file first. 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. the filename (fn) needs to be in the current working directory - often that is the directory from which you started coot. 2. Would it be possible to add additional point to improve the “guidance” of the path? Yes, it's possible. 2. Perhaps as part of a script? All of Coot's HOLE functions are scriptable. 2. Currently the path tends to take less obvious paths because only two points along the path can be specified, It might be that - or it might be a bug. Or maybe the step size is too big. 2. 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. indeed - from the figure that I attached, you can see that the algorithm is supposed to handle paths that are not straight lines. 2. 3. Do I just need to cite coot and HOLE or also additional references for the HOLE implementation? Coot and HOLE would be fine. I don't think that I wrote it up formally (probably because it was largely (just) an implementation of Oliver's paper). I'd like it to carve out the path from a map and add arbitrary map caps - that might be worth a mention. 3. 4. 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. Isn't this just a matter of undisplaying or closing the previous generic objects? Paul. 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/
Re: [COOT] HOLE pore radius in coot
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 "", line 1, in
File "C:/Work/IpT/Cryosparc/HOLE/April_2022/Local/coot_hole.py", line 4, in
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
Sent: May 22, 2022 11:56 PM
To: Omid Haji-Ghassemi ; 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)
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/
[COOT] HOLE pore radius in coot
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/
