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: [log in to unmask]
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