As it turns out, there is indeed such a function (thanks Paul!) -
seqnum_from_serial_number(), which takes the molecule, chain id and serial
number (where the serial number is a sequential id for each residue in a chain,
starting at 0). And there is another function, chain_n_residues() which will
give the number of residues in a chain.
So we can make functions to get the first and last residues of an all-protein
chain pretty easily, something like:
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
Unfortunately this doesn’t work as well when solvent molecules are present in
the same chain as the protein, as they will be counted by chain_n_residues.
Oliver.
On Dec 29, 2013, at 1:56 PM, Oliver Clarke <[email protected]> wrote:
> Also - apologies for all the questions - is there any way to easily get the
> first and last residue of a given chain from the scripting interface?
>
> This would be handy for scripting using functions that take a residue range
> where one might want to apply the function to an entire arbitrary chain (e.g.
> fit_residue_range_to_map_by_simplex or score_residue_range_fit_to_map).
>
> Cheers,
> Oliver.
>
>
> On Dec 29, 2013, at 1:34 PM, Oliver Clarke <[email protected]> wrote:
>
>> Maybe something like this - where by default it just does a rigid body, but
>> if morph is set to “Y” it does a more extensive morph at three different
>> radii:
>>
>> set_refinement_immediate_replacement(1) #Accept rigid body without prompting.
>> mol_id=13 #Which molecule should we modify?
>> r1=20
>> r2=10
>> r3=5
>> r1_cycles=10
>> r2_cycles=5
>> r3_cycles=5
>> morph="N" #Do extensive morph?
>> do_rigid="Y"
>> if do_rigid=="Y":
>> for ch_id in chain_ids(mol_id): #Rigid body refine each chain first.
>> rigid_body_refine_by_atom_selection(mol_id, "//%s//"%(ch_id))
>> accept_regularizement()
>> if morph=="Y": #Sequential morph_chain at three radii.
>> for ch_id in chain_ids(mol_id):
>> for n1 in range(1,r1_cycles):
>> morph_fit_chain(mol_id, "%s"%(ch_id), r1)
>> for n2 in range(1,r2_cycles):
>> morph_fit_chain(mol_id, "%s"%(ch_id), r2)
>> for n3 in range(1,r3_cycles):
>> morph_fit_chain(mol_id, "%s"%(ch_id), r3)
>> set_refinement_immediate_replacement(0) #Return to default behavior.
>>
>>
>> On Dec 29, 2013, at 9:51 AM, Oliver Clarke <[email protected]> wrote:
>>
>>> Thanks Paul - Initially I tried rigid body + 10 cycles of morph_fit_chain
>>> at a radius of 11 Å - that seemed to work better than rigid body alone,
>>> although some of the larger domain shifts are still not corrected.
>>>
>>> Perhaps I need a larger radius for that - I’ll try doing 10 cycles at a
>>> radius of 20 Å, followed by 5 each at 10 Å and 5 Å.
>>>
>>> Regarding blurred maps, is there any way to adjust the sharpening factor on
>>> the fly in a script, in such a manner that it can be returned to normal
>>> afterwards?
>>>
>>> Also, Coot seems to write out a copy of the pdb to the coot-backup
>>> directory after every cycle of morph_chain - is there any way to turn off
>>> this behavior? Normally it would be fine, but with a few hundred operations
>>> that adds up to several GB of backup files, which probably slows down the
>>> whole process somewhat.
>>>
>>> Cheers,
>>> Oliver.
>>> On Dec 29, 2013, at 6:21 AM, Paul Emsley <[email protected]> wrote:
>>>
>>>> On 29/12/13 02:51, Oliver Clarke wrote:
>>>>>
>>>>>
>>>>> I agree that normally rigid body refinement of each chain wouldn’t be
>>>>> very useful - I’m using this script in a situation where we have a large
>>>>> complex of many subunits that we need to fit to a quite low-resolution
>>>>> map (of a related complex from another species),
>>>>
>>>> Sounds familiar :-) (... as may be apparent at the Study Weekend).
>>>>
>>>>> and an initial round of rigid body fitting seemed to be helpful on
>>>>> individual chains but was quite laborious when performed manually for
>>>>> each chain.
>>>>
>>>> Eeek. Yes...
>>>>
>>>> Also consider Jiggle Fit.
>>>>
>>>>> This script seemed to help with that, and I was adding morph_fit_chain in
>>>>> the hope that it would correct errors in the curvature of helices, or the
>>>>> orientation of two domains within a multi-domain protein.
>>>>
>>>> OK, for the orientation of domains you need a larger radius, performed on
>>>> the chain. For the curvature of helices you need (I would imagine) a
>>>> smaller radius performed on a residue selection.
>>>>
>>>>>
>>>>> Yes, that was the problem - It works when I replace chain_id with ch_id.
>>>>>
>>>>
>>>> good.
>>>>
>>>>> So you would suggest calling morph_chain several times in succession?
>>>>
>>>> Definitely. That and the residue selection version.
>>>>
>>>>> That makes sense, because the modifications from one round were quite
>>>>> subtle. I’ll give it a go with 5-10 rounds and see how it works.
>>>>>
>>>>>
>>>>
>>>> Also, I found that fitting into blurred maps at the early stages (large
>>>> radius) was beneficial.
>>>>
>>>> It is not yet clear to me what's the best relationship of the round
>>>> number, resolution, and the radii.
>>>>
>>>> Paul.
>>>>
>>>>
>>>> <morph-residues-gui.scm>
>>>
>>
>
