"N" and "C" works fine for me. Actually "auto" as well, but what is
missing is a resorting of the residues (they are in the wrong order
after addition). So, do a
sort_residues(imol)
after addition and everything will be fine.
B
On 29/04/2014 15:08, Oliver Clarke wrote:
Hi Bernhard,
Thanks, but I’m not sure that’s the case - in the scheme manual that
parameter is listed as residue_type, same as for
add_terminal_residue, and in any case when I change it to “N” it
still adds at the C-terminus.
Also, even when adding at the C-terminus, it adds after the TER flag
and whatever solvent molecules are part of the chain, which does not
seem like the desired behaviour.
Best, Oliver. On Apr 29, 2014, at 2:45 AM, Bernhard Lohkamp
<bernhard.lohk...@ki.se> wrote:
I believe what you call res_type is rather actually term_type and
this function doesnt take "auto", only "N" and "C". So I am afraid
you have to specify yourself which end you want to add.
HTH,
B
On 28/04/2014 21:33, Oliver Clarke wrote:
Hi all,
I’ve used the add_terminal_residue_using_phi_psi function to make
a little shortcut to force Coot to add a terminal residue (code
below), which I can then refine into the density (sometimes Coot
cannot find an acceptable position for a terminal residue, when I
can clearly see appropriate density).
It works fine, except that there seems to be a bug in
add_terminal_residue_using_phi_psi - it always adds the new
residue at the end of the chain, regardless of whether the N-term
or C-term residue is clicked, and it also adds after the TER flag
if present. This means that I can’t use this to add residues to
the N-term, as Coot will not recognize that the adjacent residues
are linked if they are not adjacent in the file. Thoughts?
Oli.
#Force addition of residue - useful when #Coot says "No
acceptable position found" # but density is clear. def
force_add_terminal_residue(): def force_addition(res1):
mol_id=res1[1] ch_id=res1[2] res_no=res1[3] res_type="auto"
add_terminal_residue_using_phi_psi(mol_id,ch_id,res_no,
res_type,-64,-41) user_defined_click(1,force_addition)
add_simple_coot_menu_menuitem(menu, "Forced addition of terminal
residue (click terminus)", lambda func:
force_add_terminal_residue())
-- ***************************************************
Dr. Bernhard Lohkamp Associate Professor/Docent 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:
bernhard.lohk...@ki.se
--
***************************************************
Dr. Bernhard Lohkamp
Associate Professor/Docent
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: bernhard.lohk...@ki.se
