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 <[email protected]> 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: [email protected]
