[phenixbb] excluding atoms from refinement

[Pavel Afonine]

Hi Crystal,

note that Jeff's suggestion will exclude selected atoms from refinement 
of coordinates *only*. The other parameters, such as B-factors, 
occupancies etc will still be refined for them. More complete is:

   refine {
     strategy = *individual_sites *individual_sites_real_space rigid_body \
                *individual_adp group_adp tls *occupancies group_anomalous
     sites {
       individual = not (chain B and resseq 13:15)
     }
     adp {
       individual {
         isotropic = not (chain B and resseq 13:15)
         anisotropic = not all
       }
     }
     occupancies {
       remove_selection = not (chain B and resseq 13:15)
     }
   }

Depending on whether you want these atoms to participate in bulk-solvent 
mask calculation you may set up the occupancies of selected atoms to zero.

Pavel


On 12/8/11 10:29 AM, Jeff Headd wrote:
> Hi Crystal,
>
> You can exclude any part of your model with a selection like this:
>
> refinement {
>    refine {
>      strategy = *individual_sites *individual_sites_real_space rigid_body \
>                 *individual_adp group_adp tls *occupancies group_anomalous
>      sites {
>        individual = "not chain B"
>        torsion_angles = None
>        rigid_body = None
>      }
>    }
> }
>
> In this example, I've excluded chain B from individual site
> refinement. You can see more selection examples here:
>
> http://www.phenix-online.org/documentation/refinement.htm#anch88
>
> Thanks,
> Jeff
>
> On Thu, Dec 8, 2011 at 10:21 AM, Crystal VanderZanden
> <Crystal.Vanderzanden at colostate.edu>  wrote:
>> Does anybody know if there a general code that will allow us to exclude
>> something from refinement?  I would like to specify that there is a
>> particular part of my structure that I don't want to refine the position.
>> I've thought about deleting those atoms from the pdb file, but then that
>> phasing information is excluded from the refinement.  Any ideas?
>>
>> Thanks,
>> Crystal
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