Cablam example


CaBLAM stands for C-Alpha Based Low-resolution Annotation Method. It is a system designed to use protein CA geometry to evaluate mainchain geometry and identify areas of probable secondary structure. CaBLAM is intended for use in low-resolution structures where compound errors or ambiguities in a model may make the results of highly-sensitive measures of protein conformation, such as Ramachandran analysis, difficult or impossible to interpret. CaBLAM validation is available in MolProbity or in the PHENIX suite.

For each residue, cablam_validate calculates several measures based on CA geometry. It uses these measures as coordinates for comparison against contours of expected protein behavior derived from a high-quality dataset (Top8000). Residues that fall outside these contours are considered outliers and are reported in validation feedback.

cablam_validate also compares local CA geometry measures which are robust at low resolution against contours of expected secondary structure behavior. Residues that fall within these secondary structure contours are reported as probable members of that secondary structure type.

Read more about how CaBLAM works in this PHENIX newsletter.