Differential density peaks and hydrophobic residues
Hi everyone, I am refining a ~3A structure using phenix 1.21.2-5419. I am at the final stages of the refinement but I am seeing some positive density on some hydrophobic residues (mainly Ile and Leu) together with a negative density around those residues (image attached). At first, I guessed that might be related to solvent mask, so I turned on optimize_mask. That did not solve the issue, although slightly decreased R values. Diffraction data was processed with autoproc+staraniso and does not seem to be twinned (normal intensity stats + map deteriorates if twinning refinement is applied). Does anyone have a guess about that? Best, Lucas -- Lucas Souza dos Santos Laboratório de Biologia Estrutural Aplicada (LBEA) Departamento de Microbiologia Instituto de Ciências Biomédicas II - USP Cidade Universitária - São Paulo - SP CEP 05508-000
Hi, It would be helpful to see the xyz, B and Occ parameters for the atoms in the positive difference density peaks. Thanks, Dale Tronrud On 3/26/2025 8:04 PM, Lucas Souza wrote:
Hi everyone,
I am refining a ~3A structure using phenix 1.21.2-5419. I am at the final stages of the refinement but I am seeing some positive density on some hydrophobic residues (mainly Ile and Leu) together with a negative density around those residues (image attached). At first, I guessed that might be related to solvent mask, so I turned on optimize_mask. That did not solve the issue, although slightly decreased R values. Diffraction data was processed with autoproc+staraniso and does not seem to be twinned (normal intensity stats + map deteriorates if twinning refinement is applied).
Does anyone have a guess about that?
Best, Lucas
-- Lucas Souza dos Santos Laboratório de Biologia Estrutural Aplicada (LBEA) Departamento de Microbiologia Instituto de Ciências Biomédicas II - USP Cidade Universitária - São Paulo - SP CEP 05508-000
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Hi Lucas, this is odd. I can have a look if you send me the model and data files (off-list). As Dale suggested, this looks like xyz/B/occupancy aren't correct for these atoms. Pavel On 3/26/25 20:04, Lucas Souza wrote:
Hi everyone,
I am refining a ~3A structure using phenix 1.21.2-5419. I am at the final stages of the refinement but I am seeing some positive density on some hydrophobic residues (mainly Ile and Leu) together with a negative density around those residues (image attached). At first, I guessed that might be related to solvent mask, so I turned on optimize_mask. That did not solve the issue, although slightly decreased R values. Diffraction data was processed with autoproc+staraniso and does not seem to be twinned (normal intensity stats + map deteriorates if twinning refinement is applied).
Does anyone have a guess about that?
Best, Lucas
-- Lucas Souza dos Santos Laboratório de Biologia Estrutural Aplicada (LBEA) Departamento de Microbiologia Instituto de Ciências Biomédicas II - USP Cidade Universitária - São Paulo - SP CEP 05508-000
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Hey,
Looks like a wrong fit model. You can check this is the only error. Over
all model quality and processing statistics and refinement statistics.
On Fri, 4 Apr 2025, 11:36 am Pavel Afonine,
Hi Lucas,
this is odd. I can have a look if you send me the model and data files (off-list). As Dale suggested, this looks like xyz/B/occupancy aren't correct for these atoms.
Pavel
On 3/26/25 20:04, Lucas Souza wrote:
Hi everyone,
I am refining a ~3A structure using phenix 1.21.2-5419. I am at the final stages of the refinement but I am seeing some positive density on some hydrophobic residues (mainly Ile and Leu) together with a negative density around those residues (image attached). At first, I guessed that might be related to solvent mask, so I turned on optimize_mask. That did not solve the issue, although slightly decreased R values. Diffraction data was processed with autoproc+staraniso and does not seem to be twinned (normal intensity stats + map deteriorates if twinning refinement is applied).
Does anyone have a guess about that?
Best, Lucas
-- Lucas Souza dos Santos Laboratório de Biologia Estrutural Aplicada (LBEA) Departamento de Microbiologia Instituto de Ciências Biomédicas II - USP Cidade Universitária - São Paulo - SP CEP 05508-000
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participants (4)
-
Dale Tronrud -
Lucas Souza -
Pavel Afonine -
Smita Yadav