[phenixbb] syntax and alternate conformations

Mark Collins mcollins at convex.hhmi.columbia.edu
Tue May 27 21:28:29 PDT 2008


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 1) I see from the parameters file that you are using an outdated  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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