Aha, didn’t know about sort_residues() - great, works now, thanks Bernhard!
Oliver. On Apr 29, 2014, at 9:27 AM, Bernhard Lohkamp <bernhard.lohk...@ki.se> wrote: > > "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
