Hi Jason, In your AutoBuild_run_1_/ directory there should be a file like: cycle_best_3.log or something that is the model-building log file for the best model built. This should contain lines like: --SIDE CHAIN DENSITY/RMS-- RESIDUE CC Z-SCORE AVG MIN MAX A 37 LEU 0.84 1.81 1.83 0.92 2.76 A 38 GLY 0.83 3.03 A 39 ASN 0.64 0.83 1.35 0.86 2.08 A 40 GLU 0.47 0.11 0.64 -0.28 1.86 A 41 TYR 0.15 -1.31 -0.06 -0.86 0.83 TRUNCATED AT CB which will have the text TRUNCATED AT CB at truncated residues in parts of the model that are otherwise assigned to sequence. So you could find those all with: grep 'TRUNCATED' cycle_best_3.pdb Additionally, some of the residues that are at the end of your PDB file may be not assigned to sequence at all. They are indicated like this in that log file: FRAGMENT (UNPLACED) WITH 20 ATOMS. MEAN RHO: 2.32 Z-SCORE: 0.45 A 111 ARG 0.64 1.72 1.58 0.36 2.54 A 112 LEU 0.71 1.15 1.96 1.41 3.14 A 113 VAL 0.78 1.63 1.50 0.93 2.31 A 114 PRO 0.61 1.66 0.63 0.25 1.13 All the best, Tom T

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Hi,

I have a pdb file obtained from autobuild. However, some of the sidechains are missing. Is there an easy way to detect which sidechains are missing? The reason I am asking is my pdb file is huge. It takes a lot of effort to go through one reside by one residue. Thanks.

-- ====================== Jason Structural Biology Department University of Pittsburgh ====================== _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb