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 <[log in to unmask]> 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
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