Thanks Bernhard, that’s very helpful.
Using that function, I wrote a little script that will delete a chain based on
the currently selected residue:
def first_residue(mol_id,ch_id):
result=seqnum_from_serial_number(mol_id,"%s"%(ch_id),0)
return result
def last_residue(mol_id,ch_id):
n=chain_n_residues(ch_id,mol_id)-1
result=seqnum_from_serial_number(mol_id,"%s"%(ch_id),n)
return result
active_mol_id=active_residue()[0]
active_chain_id=active_residue()[1]
first_res=first_residue(active_mol_id,active_chain_id)
last_res=last_residue(active_mol_id,active_chain_id)
delete_residue_range(active_mol_id,active_chain_id,first_res,last_res)
I’d quite like to assign this to a button, but the user defined button
interface in coot only seems to take one-line commands, not multi-line - I
guess I can assign it to a key binding though. Or is there an easy way to add a
user-defined menu item?
Oliver.
On Mar 12, 2014, at 3:08 AM, Bernhard Lohkamp <bernhard.lohk...@ki.se> wrote:
>
> Hi Oliver,
>
> You can use the scripting function delete_residue_range
> (https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#index-delete_002dresidue_002drange-709):
>
> delete_residue_range(imol, chain_id, start_res, stop_res)
>
> Maybe not exactly what you want, but that works fine for this purpose (*).
> You can give a residue range outside what you have, just to make sure
> everything is deleted, i.e. delete_residue_range(0,"A", -100,100000).
>
> B
>
> (*) Incidentally it has been on my todo list for quite some time to make a
> delete chain (etc) function...
>
> On 12/03/2014 00:51, Oliver Clarke wrote:
>> Another one to chalk on the list of things that would be nice to have but
>> not really needed - I feel like having a delete chain option in the ‘Delete
>> item’ dialog would be very handy…
>>
>> I often find myself needing to delete a chain (from a complex or oligomer
>> for example), and I always switch the color to Jone’s Rainbow and then hunt
>> around for the N- and C- termini and use delete zone, which works but is a
>> little cumbersome.
>>
>> Being able to click on a single atom from the desired chain to delete it
>> would speed things up tremendously, for example when editing the kind of
>> spaghetti-model that sometimes comes out of buccaneer or Arp/warp at low
>> resolution (where there a lot of peptide fragments that need cleaning up).
>>
>> Best,
>> Oliver.
>>
>
> --
> ***************************************************
>
> 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
