[phenixbb] occupancy refinement

[Marco Bellinzoni]

Dear Pavel,

your trick seems to me potentially 'dangerous', though: if you assign an 
altloc identifier to a whole residue, its atoms won't 'see' any other 
atom that does have a different altloc identifier because it is like 
they don't exist at the same time - is this right? If so, in principle, 
a sulfate labelled with an altloc identifier 'A' should not see 
neighbouring atoms which are labelled as altloc 'B', which may well be 
the whole side chain of a residue in close contact, modelled in double 
conformation. That way, no restraints will be applied on close non 
bonded atoms, etc...

Or am I missing something?

Thanks,
Marco

Pavel Afonine wrote:
> Hi Marco and Christian,
>
> another trick that I think will work is to assign a non-blanc altloc 
> identifier to each SO4 ion. For example:
>
> HETATM 5269  S  ASO4   601      88.394   7.885  58.375  1.00 
> 26.69           S
> HETATM 5270  O1 ASO4   601      88.709   6.482  58.612  1.00 
> 26.69           O
> HETATM 5271  O2 ASO4   601      88.383   8.143  56.832  1.00 
> 26.69           O
> HETATM 5272  O3 ASO4   601      89.311   8.886  58.913  1.00 
> 26.69           O
> HETATM 5273  O4 ASO4   601      87.037   8.083  58.916  1.00 
> 26.69           O
> HETATM 5274  S  ASO4   602     123.263  -1.833  44.610  1.00 
> 41.54           S
> HETATM 5275  O1 ASO4   602     123.408  -1.546  46.092  1.00 
> 41.54           O
> HETATM 5276  O2 ASO4   602     124.616  -2.116  44.068  1.00 
> 41.54           O
> HETATM 5277  O3 ASO4   602     122.687  -0.633  43.944  1.00 
> 41.54           O
> HETATM 5278  O4 ASO4   602     122.349  -3.008  44.466  1.00 
> 41.54           O
>
> so one occupancy factor will be refined per each ion, and it will be 
> constrained between 0 and 1.0.
>
> Pavel.
>
>
> On 1/27/10 1:14 AM, Marco Bellinzoni wrote:
>> Hi Christian,
>>
>> all you have to do is to define each sulfate as a constrained group 
>> for occupancy refinement, like this:
>>
>> constrained_group {
>>        selection = "chain C and resid x"
>>      }
>>      constrained_group {
>>        selection = "chain C and resid y"
>>      }
>>
>> where resid is simply the residue number. The occupancy of all atoms 
>> that belong to the same constrained group will be refined to the same 
>> value.
>>
>> Best wishes,
>> Marco
>>
>> Christian Roth wrote:
>>> Dear all,
>>> I refine a structure of a protein to 1.4 A and found a few 
>>> SO4-Ions.  I tried to refine this sulfurs and some of these seems to 
>>> be not fully occupied, as the negative difference density suggest. I 
>>> tried to refine the occupancy of the sulfate ions to get an idea how 
>>> strong the different binding sites might be occupied. All sulfate 
>>> ions are in Chain C of my pdb. I tried to refine the occupancy 
>>> individually using refine.occupancy.individual SO4 but this lead to 
>>> different occupnacies for every atom for every atom and theix cant 
>>> be the case for sure.  Then I tried and group occupancy  with 
>>> resname=SO4 but now every sulfate ion has the same occupancy, which 
>>> is indicated from my previous refinements  also not the case, 
>>> because two ions have no negative difference density. At the momentI 
>>> can not figure out how I should combine the keywords for the 
>>> individual occupancy refinement of the different sulfate ions. In my 
>>> structure. Should I define for every ion a different chain or how I 
>>> could overcome this problem?
>>> I would be very happy if anyone has a idea to sove this problem or 
>>> tell me what keyword I misunderstood in the documentation.
>>>
>>> Best regards
>>> Christian
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>   
>>
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-- 
================================
Marco Bellinzoni
Unité de Biochimie Structurale
Institut Pasteur
25, rue du Dr. Roux
75724 Paris Cedex 15
France
Tel. +33 (0)1 45688608
Fax. +33 (0)1 45688604
================================