[phenixbb] syntax and alternate conformations

[Pavel Afonine]

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1) I see from the parameters file that you are using an outdated version 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