Re: [phenixbb] real space residuals

HI, oh, I see, residuals are of course different. What do you need them for? We have at least two real-space target types. This is not exposed to user-accessible level, though you can compute these target values using a Python script. One is just a sum of density map values at interpolated at atomic centers. The other one is a squared sum of differences (rho_target-rho_model). Pavel On 9/26/11 1:04 PM, Nathaniel Echols wrote:

These all output correlation coefficients, not residuals.

On Mon, Sep 26, 2011 at 1:02 PM, Pavel Afonine wrote:

...

Hi,

option 1:

phenix.model_vs_data model.pdb data.mtz comprehensive=true

will output map CC per atom or per residue.

option 2:

phenix.real_space_correlation

can be used if more fine-tuning is needed.

option 3:

phenix.get_cc_mtz_mtz and phenix.get_cc_mtz_pdb

Also, it is under 30 lines of Python code if using CCTBX.

Pavel

On 9/26/11 12:56 PM, Bradley Hintze wrote:

Hey phenix, I see a util for real space correlation. Real space residuals are slightly different. Is the a tool to calculate RSR in phenix?

-- Bradley J. Hintze Duke University Graduate Student Department of Biochemistry

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