Hello Dmitry,

Depending on the resolution of the map of the whole complex, you might need to apply secondary structure restraints or reference model restraints (to prevent the atomic models from deviating too much from their starting coordinates), or you might even need to only do rigid-body refinement.

Without knowing the resolution range of this map, it is difficult to advise on a strategy.

Cheers,

Guillaume


On 24 Oct 2024, at 13:28, Dmitry Semchonok <[email protected]> wrote:

Dear Colleagues,
We're encountering an issue with composite model refinement and would appreciate your advice.

Our scenario:
  1. We built two separate models based on two subtracted maps of a single complex.
  2. We have a lower-resolution map of the full complex.
  3. We merged the two models into the full complex and refined it against the full map.
The problem:
When refining the merged model against the full map using real-space refinement in Phenix, the clashscore progressively worsens.
Has anyone experienced similar issues, or can you offer suggestions on addressing this problem?

Thank you for your insights.

Best regards,
Dmitry


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