Hi Xin,
Predict and build uses process predicted model to estimate suitable VRMS
values from the pLDDT values in a processed chain to be used in MR.
Process predicted model first converts average pLDDT to estimated RMS error
using an empirical formula from RoseTTAFold:
rmsd_est = 1.5 * exp(4*(0.7-pLDDT)) where pLDDT is fractional (0 to 1)
Then it uses a second empirical formula to suggest a value of VRMS based on
the RMS error:
vrms = vrms_from_rmsd_slope * rms + vrms_from_rmsd_intercept
where the slope is 1 and intercept is 0.25 A.
All the best,
Tom T
On Sun, Aug 10, 2025 at 9:49 PM [email protected]
Dear All, I hope this email finds you well. While reviewing the MR-related output files generated by Phenix PredictAndBuild (see attached screenshot), I noticed that an RMS value is set in the Phaser input section. I found that in certain cases this parameter can have a significant impact on MR results. Could you kindly advise how this RMS value is determined or calculated within Phenix PredictAndBuild? [??????] Thank you very much for your time and guidance.
Best regards,
Xin Zhang
School of Biomedical Sciences,
The University of Hong Kong
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