[phenixbb] A few questions

[Pavel Afonine]

Hi Paul,

currently phenix.refine can refine occupancies as: individual, 
constrained individual and group.

- In individual occupancy refinement occupancy of each atom is refined 
individually.
- In constrained individual occupancy refinement occupancies of each 
atom are refined "individually" but it is made sure that the sum of them 
is one (for each atom, not group of atoms).
- In group occupancy refinement you can refine one occupancy per 
selected group of atoms, without any constrains.

What you mention is "constrained group occupancy refinement" where you 
refine one "individual" occupancy per group of atoms making sure that 
the sum of them is one. Unfortunately this is not implemented. This is 
on the top of my to-do list, so hopefully we will have it soon.

Pavel.


Paul Adams wrote:
> Hi Pavel,
>
>    the occupancy should be the same for all of the atoms in an  
> alternate conformation (grouped occupancy refinement). I doesn't make  
> chemical sense for bonded atoms to have different occupancies.
>
>    Cheers,
> 	Paul
>
> On Feb 6, 2008, at 8:56 AM, Pavel Afonine wrote:
>
>   
>> Hi Christopher,
>>
>> thanks for your questions!
>>
>>     
>>> We are working on a refinement at 1.14A which was suffering from  
>>> lots of NPD atoms when refined anisotropically with refmac5 and/or  
>>> shelx.
>>>       
>> The implementation of anisotropic B-factors refinement in  
>> phenix.refine
>> should never lead to non-positive definite ADP matrices or any
>> "instability" in refinement.
>>
>>     
>>> 1. In our model we have a few solvent ligands, and these show up  
>>> in the log file as:
>>>           Unusual residues: {'EDO': 11, ' CL': 1, 'SO4': 1}
>>>           Classifications: {'undetermined': 13, 'water': 437}
>>> We've used a cif file for EDO with H's when needed, but still see  
>>> this message. Is this normal? What is unusual?
>>>
>>>       
>> Yes, it is normal. In this context "unusual" means that this is not
>> "usual amino acid, water, dna/rna fragment".
>>
>>     
>>> 2. When choosing "indivdual_occupancies" for the refinement, all  
>>> the atoms within an alt-conf are refined to different occupancies-  
>>> is this expected? It seems that all atoms in the A conf should  
>>> have the same value, and the occ of all atoms in the B conf should  
>>> also be the same. Instead, we see this:
>>> ATOM    232  CA AGLU A  28      26.163   7.163   4.422  0.77   
>>> 6.73           C
>>> ATOM    233  CB AGLU A  28      24.851   7.269   3.672  0.80   
>>> 9.27           C
>>> ATOM    234  CG AGLU A  28      24.978   6.767   2.259  0.66  
>>> 12.91           C
>>> ATOM    235  CD AGLU A  28      23.662   6.717   1.554  1.00  
>>> 16.51           C
>>> ATOM    236  OE1AGLU A  28      22.874   7.667   1.757  0.71  
>>> 18.78           O
>>> ATOM    237  OE2AGLU A  28      23.429   5.733   0.803  0.60  
>>> 16.77           O
>>> ATOM    240  CA BGLU A  28      26.140   7.156   4.424  0.23   
>>> 6.33           C
>>> ATOM    241  CB BGLU A  28      24.794   7.230   3.713  0.20   
>>> 6.48           C
>>> ATOM    242  CG BGLU A  28      24.877   6.766   2.280  0.34   
>>> 6.55           C
>>> ATOM    243  CD BGLU A  28      23.536   6.702   1.598  0.00   
>>> 7.53           C
>>> ATOM    244  OE1BGLU A  28      23.497   7.014   0.381  0.29   
>>> 7.85           O
>>> ATOM    245  OE2BGLU A  28      22.543   6.341   2.280  0.40   
>>> 8.40           O
>>>
>>>       
>> This is correct behavior and this is exactly what you should expect
>> refining occupancies of atoms in alternative conformations: the sum of
>> occupancies of conformation A and B must be one. So, in your  
>> example above:
>>
>> ATOM 232 CA AGLU A 28 26.163 7.163 4.422 0.77 6.73 C
>> ...
>> ATOM 240 CA BGLU A 28 26.140 7.156 4.424 0.23 6.33 C
>>
>> the total occupancy is: 0.77+0.23=1
>> Same for other atoms.
>>
>>     
>>> 3. Adding hydrogens during anisotropic refinement results in the  
>>> Parvati server giving "Illegal Biso" errors for many of the  
>>> hydrogens.
>>>       
>> The H atoms at normal resolutions (not subatomic resolution) are  
>> treated
>> as a special case. For example (default behavior), they ride on bonded
>> atoms during coordinates refinement (riding model, distances X-H do  
>> not
>> change), we refine one occupancy and isotropic B-factor per all H  
>> atoms
>> in your molecule, etc. I don't know what exactly "Illegal Biso"  
>> means in
>> Parvati server, but most likely you want to exclude H atoms for this
>> analysis.
>>
>> Just a suggestion: at resolution 1.4A you can try to change the  
>> default
>> behavior for H refinement to this:
>>
>>   hydrogens {
>>     refine_adp = *one_b_per_residue one_b_per_molecule individual
>>     refine_occupancies = *one_q_per_residue one_q_per_molecule  
>> individual
>>   }
>>
>> Please let us know if you have any questions or problems!
>> Pavel.
>>
>>
>>
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>>     
>
>