C validating tutorial
C validating tutorial - tumblr dating game
This will launch a tool called "Polygon", which is used to simultaneously compare R-work, R-free, RMSD-bonds, RMSD-angles, Clashscore, and Average B factor.
It includes all the activities associated with producing high quality software: inspection, design analysis and specification analysis. Verification will help to determine whether the software is of high quality, but it will not ensure that the system is useful.The example used for this tutorial is called Protein Kinase A (3dnd).To get the requisite files open the GUI and set up the tutorial, as described here, called Protein Kinase A (validation). On the right-hand side click Validation and then select Comprehensive Validation (Mol Probity).Return to the Validation GUI window, and navigate to the list of C-beta position outliers. Do you recall this sidechain from the bond-length outlier list?Misfit sidechains will often have multiple diagnostic indicators of a problem, which is useful in easily identifying the worst offenders.Verification is concerned with whether the system is well-engineered and error-free.
Validation is the process of evaluating the final product to check whether the software meets the customer expectations and requirements.One approach that works well to fix this type of problem is to first mutate the offending residue to an alanine, and then run real-space refinement.These steps allow the C-beta position to be properly refined, without being trapped by the other misfit sidechain atoms (similar to the backrub in Ki NG).In the "Comprehensive Validation" window, browse to the tutorial directory that you specified above, and select 3as the "Input model", 3as the "Reflections file", and 3dnd.as the "Restraints (CIF)" file.This CIF file defines restraints for the ligand in 3dnd.Notice the high percentage of rotamer outliers, and large number of C-beta deviations (those combine geometry problems around the Calpha into a single measure, as explained in Lovell 2003).