[phenixbb] Problem with parameters file for group ADP refinement

Pavel Afonine PAfonine at lbl.gov
Wed Dec 30 15:17:56 PST 2009


Hi Kendall,

I guess you need to change the default setting for

group_adp_refinement_mode = *one_adp_group_per_residue \
                                  two_adp_groups_per_residue group_selection

to

group_adp_refinement_mode = one_adp_group_per_residue \
                                  two_adp_groups_per_residue 
*group_selection

and then everything will be ok, please let me know otherwise.

The parameters will look like:

refinement {
  refine {
    strategy = *individual_sites individual_sites_real_space rigid_body \
               individual_adp *group_adp *tls occupancies group_anomalous
    adp {
      group_adp_refinement_mode = one_adp_group_per_residue \
                                  two_adp_groups_per_residue 
*group_selection
      group = chain X
      group = chain A
      group = chain B
      group = chain C
      group = chain D

      tls = chain X
      tls = chain A
      tls = chain B
      tls = chain C
      tls = chain D  
      
      }}


Pavel.


On 12/30/09 12:29 PM, Kendall Nettles wrote:
> I'm trying to refine a 3.5 anstrom structure with one TLS and one ADP 
> per chain, but I keep getting the error message:
>
> "Sorry: Selections for group B-factor refinement are given, but no 
> refinement requested."
>
> The parameters file is listed below. Any suggestions?
>
> Best regards and happy New Year,
>
> Kendall Nettles
>
>
> refinement {
>   refine {
>     strategy = *individual_sites individual_sites_real_space rigid_body \
>                individual_adp *group_adp *tls occupancies group_anomalous
>     adp {
>       group = chain X
>       group = chain A
>       group = chain B
>       group = chain C
>       group = chain D
>
>       tls = chain X
>       tls = chain A
>       tls = chain B
>       tls = chain C
>       tls = chain D  
>       
>       }}
>
>   
>      target_weights {
>     mode = *every_macro_cycle
>     optimize_wxc=true
>     optimize_wxu=true}
>
> }
>
> refinement.modify_start_model.adp.set_b_iso = 80
>
> refinement.input.xray_data.labels=IMEAN
>
>
> ------------------------------------------------------------------------
>
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