You appear to be mixing syntaxes for the scripting languages. Maybe
first make sure you are using pure python...
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Python_to_Scheme_and_return
..and yes, try the Extensions and make sure you have consistent master
chains.
B
Dear all,
I am working with a 4-fold NCS. Chain A has residues 273 through 278
pretty messed up, but those residues from Chain B seem to fit pretty
well the density for Chain A (as seem by NCS Ghost Control). Hence I
would to replace residues 273-278 of Chain A by those of Chain B with
appropriate rotation(s)-translation(s).
After looking Coot's manual it seems that I need to use a script (the
GUI would also change Chains C and D which I do not want), namely
copy-residue-range-from-ncs-master-to-chains. From the example I think
that I would need something like:
(copy-residue-range-from-ncs-master-to-chains 0 "B" 273 278 (list "A"))
but since I have a python Coot, I am unsure what to use. I tried without
success* the following:
copy-residue-range-from-ncs-master-to-chains(0,"B",273,278,(list "A"))
copy-residue-range-from-ncs-master-to-chains(0,"B",273,278,"A")
copy-residue-range-from-ncs-master-to-chains(0,"B",273,278,list("A"))
Hence, I would greatly appreciate some advice on the proper syntax for
the command in Python (or on the right/better way of fixing the mess in
Chain A).
Thank you for your time and help.
Regards,
Davi
* - Results of running scripts in the command window:
BL INFO:: command input is:
copy-residue-range-from-ncs-master-to-chains(0,"B",273,278,(list "A"))
Traceback (most recent call last):
File "C:\WinCoot\share\coot\python\coot_gui.py", line 209, in
do_function
guile_function = test_and_translate_guile(entry_text)
File "C:\WinCoot\share\coot\python\coot_gui.py", line 166, in
test_and_translate_guile
exec python_function in locals()
File "<string>", line 1
copy_residue_range_from_ncs_master_to_chains(0,"B",273,278,(list(*arg)
^
SyntaxError: unexpected EOF while parsing
and
BL INFO:: command input is:
copy-residue-range-from-ncs-master-to-chains(0,"B",273,278,"A")
Traceback (most recent call last):
File "C:\WinCoot\share\coot\python\coot_gui.py", line 209, in
do_function
guile_function = test_and_translate_guile(entry_text)
File "C:\WinCoot\share\coot\python\coot_gui.py", line 166, in
test_and_translate_guile
exec python_function in locals()
File "<string>", line 1
copy_residue_range_from_ncs_master_to_chains(0,"B",273,278,"A"(*arg)
^
SyntaxError: unexpected EOF while parsing
and
BL INFO:: command input is:
copy-residue-range-from-ncs-master-to-chains(0,"B",273,278,list("A"))
Traceback (most recent call last):
File "C:\WinCoot\share\coot\python\coot_gui.py", line 209, in
do_function
guile_function = test_and_translate_guile(entry_text)
File "C:\WinCoot\share\coot\python\coot_gui.py", line 166, in
test_and_transla
te_guile
exec python_function in locals()
File "<string>", line 1
copy_residue_range_from_ncs_master_to_chains(0,"B",273,278,list("A"(*arg)
^
SyntaxError: unexpected EOF while parsing
--
***************************************************
Dr. Bernhard Lohkamp
Assistant Professor
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487651
fax: (+46) 08-327626
email: [email protected]
