[phenixbb] syntax and alternate conformations

[Mark Collins]

The new download works like a dream.  The occupancy of residues with  
alternate conformations now sum to 1, using *occupancy in my script.   
Thank you once again, Mark


On May 28, 2008, at 12:28 AM, 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 1) I see from the parameters file that you are using an outdated  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
>
>
>
>
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