Hi,
I would like to get secondary structure information from a PyMol file. I
know that the following command gives a long list of every residue:
>> iterate <object name> & n. ca, print resn,resi,ss
I found the following script, that gives you a more "condensed" list (see
below):
>> PyMOL>@../..\ss.pml
>> PyMOL>class SSList:\
>> PyMOL>list = []\
>> PyMOL>def purge( self, resi, ss ):\
>> PyMOL>if not self.list or self.list[-1][0] != ss:\
>> PyMOL>self.list.append( [ss, resi, resi ] )\
>> PyMOL>else:\
>> PyMOL>self.list[-1][2] = resi\
>> PyMOL>def __repr__( self ):\
>> PyMOL>return "\n".join( map( self.repr_item, self.list ) )\
>> PyMOL>def repr_item( self, item ):\
>> PyMOL>return item[0]+" ("+item[1]+"-"+item[2]+")"
>> PyMOL>sslist = SSList()
>> PyMOL>cmd.iterate( "n. ca", "sslist.purge( resi, ss )" )
>> PyMOL>print sslist
>> L (2-3)
>> H (4-14)
>> L (15-23)
>> H (24-44)
>> L (45-50)
>> H (51-72)
>> L (73-73)
>> H (74-84)
>> L (85-86)
I have two problems: the command >> PyMOL>@../..\ss.pml << gives the
following answer in PyMol: "No such file or directory"
When I leave this command away, and I copy & paste the initial iteration
followed by the script,
iterate SH3 & n. ca, print resn,resi,ss
class SSList:\
list = []\
def purge( self, resi, ss ):\
if not self.list or self.list[-1][0] != ss:\
self.list.append( [ss, resi, resi ] )\
else:\
self.list[-1][2] = resi\
def __repr__( self ):\
return "\n".join( map( self.repr_item, self.list ) )\
def repr_item( self, item ):\
return item[0]+" ("+item[1]+"-"+item[2]+")"
sslist = SSList()
cmd.iterate( "n. ca", "sslist.purge( resi, ss )" )
print sslist
PyMol gives me the following answer:
Iterate: iterated over 68 atoms.
<pymol.SSList instance at 0x000000000688C648>
I still get the long list with every single residue mentioned, but not the
desired "condensed" form.
Maybe I just don't know how to print the list on the screen. Or is there
more about it?
Thanks for any help,
Ferdi
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