Re: [phenixbb] excluding atoms from refinement

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 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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