Re: [COOT] Help needed with copy-residue-range-from-ncs-master-to-chains

[Davi de Miranda Fonseca]

I would rather avoid using it, since (from what I understood) it would 
also replace residues 273-278 of chains C and D. Isn't this correct?

But I gave it a try, however it does not seem to change my model. Output:
INFO: operating on molecule number  2
WARNING:: failed to find master_chain_id "B" in 3 NCS ghosts
    ghost: chainid "B" has NCS master "[GHOST Name: NCS found from 
matching Chai
n B onto Chain A, chain-id: B, target-chain-id: A, displayed? 1]"
    ghost: chainid "C" has NCS master "[GHOST Name: NCS found from 
matching Chai
n C onto Chain A, chain-id: C, target-chain-id: A, displayed? 0]"
    ghost: chainid "D" has NCS master "[GHOST Name: NCS found from 
matching Chai
n D onto Chain A, chain-id: D, target-chain-id: A, displayed? 0]"
But if I try to copy residues 273-278 of chain A (bad ones) using the 
suggested extension, it works (i.e. now I have 4 pretty messed up 
chains). Is this* a bug? (* - it allows me to select a chain but it only 
works with chain A selected)
By the way, I am using Wincoot 0.7 Clayton (revision 4459) [with python 
2.6.6 embedded].

I just tried renaming/ordering the chains, performing the NCS fix in 
Coot, re-renaming/re-ordering the chains. And it worked, however it 
would be great to be able to use the 
copy-residue-range-from-ncs-master-to-chains script in the future (to 
copy select residues from any chain to any target chain(s)), hence I 
would greatly appreciate some advice on the proper syntax for the 
command in Python.

Regards,
Davi

On 14/01/2013 12:54, Francis E Reyes wrote:
Does Extensions -> NCS -> Copy NCS Residue Range not work ?

F

On Jan 14, 2013, at 12:41 PM, Davi de Miranda Fonseca <davi.fons...@ntnu.no> 
wrote:

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