[phenixbb] syntax and alternate conformations

[Pavel Afonine]

Hi Mark,

yes, group_occupancies is no longer there. By default, phenix.refine 
will refine occupancies of all atoms in alternative conformations (the 
constraints on occupancies are built automatically based on input PDB 
file).

On top of it, you can specify your own selections for group and 
individual occupancy refinement. However note, there will be no 
constraints applied to user selected occupancies.

For example, if you do:
group = chain A and resid 113
there will be one occupancy refined per residue 113 in chain A. If you 
specify multiple groups they will be treated independently.

Pavel.


On 5/27/2008 9:28 PM, Mark Collins wrote:
> Thank you both, I am currently upgrading from 1.3b-rc6 to 1.3-rc2. 
>  From both your responses I take it that there is no longer a 
> group_occupancies option but any pdb file containing residues with 
> alternate conformations will be recognized automatically the 
> group_occupancies refined?
>
> Mark
>
>
> On May 27, 2008, at 9:00 PM, Pavel Afonine wrote:
>
>> Hi Mark,
>>
>> 1) I see from the parameters file that you are using an outdated version 
>> of the program where there was a bug in occupancy refinement. Please 
>> install the latest version.
>>
>> 2) As Ralf mentioned, in the latest version the constraints for 
>> occupancies of atoms in alternative conformations are built 
>> automatically based on input PDB file. You don't need to change any 
>> parameter for this and you don't need to give selections too.
>>
>> Pavel.
>>
>>
>> On 5/27/2008 12:08 PM, Mark Collins wrote:
>>> Hi
>>> I have an unexpected result, my syntax must be incorrect.  The  
>>> relevant script commands are below, the problem is residues A113 and  
>>> B143 have alternate conformation occupancies that sums to 0.98 to  
>>> 1.06 respectively. Clearly alternate conformations of a single  
>>> residue should sum to 1 (or less than 1 possibly). Any suggestions  
>>> please?
>>> Thank you,  Mark
>>>
>>>    refine {
>>>      strategy = *individual_sites \
>>>                  rigid_body \
>>>                 *individual_adp \
>>>                  group_adp \
>>>                  tls \
>>>                  individual_occupancies \
>>>                  *group_occupancies \
>>>                  group_anomalous \
>>>
>>>     occupancies {
>>>        individual = None
>>>       group = chain A and resid 113 and altid A
>>>       group = chain A and resid 113 and altid B
>>>       group = chain B and resid 143 and altid A
>>>       group = chain B and resid 143 and altid B
>>>        }
>>> }
>>>
>>>
>>>
>>>
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>>>
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> ----------------------------------------------------------------------------------------------
> The most exciting phrase to hear in science, the one that heralds new
> discoveries, is not 'Eureka!' (I found it!) but 'That's funny ...'
> Isaac Asimov (1920 - 1992)
> ----------------------------------------------------------------------------------------------
>
> Mark Collins
> Columbia University
> Dept. of Biochemistry & Molecular Biophysics
> Hendrickson Lab, Black Building 259/201 Office/Lab
> 212 305 1951 (work)
> mnc2003 at columbia.edu <mailto:mnc2003 at columbia.edu>
>
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