[phenixbb] pdb editor after autobuild

[Thomas C. Terwilliger]

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




>> 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
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>