Troels,
Commonly I run pymol scripts by means of
run script.py
or
@ script.py
from PyMol shell!
then I use script_command ( e.g findSeq ) and further script syntax for my
tasks
e.g findSeq s.g 1f88
works perfect but
the above command for the ensemmble of pdbs give me error.
James
Dear James.
That is because there are different ways, how to get functions available in
Python.
Either you can import a script.py or you can execute it.
If you execute the script.
In Python, you would do: *execfile(script.py)*
In PyMOL, a shortcut to this is: *run script.py OR
Troels, thanks again for so detailed explanation
Firstly I've tried to use IMPORT SCRIPT and all of the above commands works
now :)
Now I'd like to understand the main sytnax of the findseq script in more
detailes.
E.g I have the set of homologues protein from wich I'd like to find triplet
Hi James.
I moved the script under the git repository yesterday, and took care of the
bug.
The script look a little different now.
So try the new one again from:
http://www.pymolwiki.org/index.php/findseqhttp://www.pymolwiki.org/index.php/Findseq
The follow the guide on the page.
# Find the
Dear PyMol Users,
I need to search defined sequence motifs in my structures.
For that purpose I've used
http://www.pymolwiki.org/index.php/FindSeq script
but when I've try to use it I've got error
PyMOLfindSeq SYG, 1a3h
Error: selName was not a string.
There was an error with a parameter.
James,
First, there's a bug in the script. It's not dealing with selName
correctly. To get around this just provide something to selName:
findSeq S.G, 1a3h, selName=found_seq
If findSeq finds the sequence, it'll return the selected atoms in found_seq.
Next, SYG is not in that protein. If you
Jason, hello!
Also I've found possible fix for that bug by lpacing this line in the 47
line of the script
if type(selName)!=(types.StringType) and type(selName)!=(types.NoneType):
By the way I've found another bug when I've tried to find the same motifs
in the several homolugues structures.
