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 
<COOT@JISCMAIL.AC.UK> 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 "<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'



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/

Reply via email to