Hello dear coot-cracks,

Sorry for bothering you again :

I could generate the .coot.py file by copying the coot.py file from 
share/coot/python/ into my home folder and adding the mentioned code:

------------

def key_binding_func_1():
     from types import ListType
     active_atom = active_residue()
     if (not active_atom):
         add_status_bar_text("No active residue")
     else:
         imol = active_atom[0]
         chain_id = active_atom[1]
         res_no = active_atom[2]
         ins_code = active_atom[3]
         atom_name = active_atom[4]
         alt_conf = active_atom[5]
         centred_residue = active_atom[1:4]
         other_residues = residues_near_residue(imol, centred_residue, 5)
         all_residues = [centred_residue]
         if (type(other_residues) is ListType):
             all_residues += other_residues
         print "imol: %s residues: %s" %(imol, all_residues)
         refine_residues(imol, all_residues)
add_key_binding("Refine residues in a sphere", "R", lambda: 
key_binding_func_1())


-----------------------------------------------------------------

However, there is this error message on starting up coot:

Loading ~/.coot.py...
Running python script /home/szueger/.coot.py
Traceback (most recent call last):
   File "<string>", line 1, in <module>
   File "/home/szueger/.coot.py", line 25, in <module>
     _coot = swig_import_helper()
   File "/home/szueger/.coot.py", line 15, in swig_import_helper
     fp, pathname, description = imp.find_module('_coot', 
[dirname(__file__)])
NameError: global name '__file__' is not defined


But this has nothing to do with the code snippet I copied at the end of 
.coot.py (right?) and I did not change anything else... ?? (I copied the 
coot.py file from share/coot/python/). Also the key binding is not displayed 
under extensions/settings/key_bindings.

This error message appears either under shared or under home environment. 
But not if I remove .coot.py.

Do I have to change something else in .coot.py?


Thanks a lot again!

Sara


PS: these are the first 25 lines from the .coot.py:

-------------------------------

from sys import version_info
if version_info >= (2,6,0):
     def swig_import_helper():
         from os.path import dirname
         import imp
         fp = None
         try:
             fp, pathname, description = imp.find_module('_coot', 
[dirname(__file__)])
         except ImportError:
             import _coot
             return _coot
         if fp is not None:
             try:
                 _mod = imp.load_module('_coot', fp, pathname, description)
             finally:
                 fp.close()
                 return _mod
     _coot = swig_import_helper()
     del swig_import_helper
else:
     import _coot
del version_info
try:
     _swig_property = property
except NameError:
     pass # Python < 2.2 doesn't have 'property'.

------------------------------------------------




On Mon, 11 Jan 2010 09:43:19 -0800
  Nathaniel Echols <[log in to unmask]> wrote:
> 2010/1/11 Sara Züger <[log in to unmask]>
> 
>> Thanks Miguel,
>>
>> but is there another way to do this sphere refinement? I'm working on a
>> shared computer and have no administrator rights and also no experience
>> with
>> python/file handling of coot.
>>
>> Or else, if there is no other way, can somebody explain me exactly what I
>> have to do/type (like copying a coot.py file into a local folder and 
>>change
>> that, but how then to tell coot to use this file?)
>>
> 
> Coot will automatically use ~/.coot.py if present - all you need to do is
> copy-and-paste Miguel's code snippet.  You don't need administrator 
>rights,
> since you're only modifying your home directory.
> 
> -Nat