[phenixbb] pdb editor after autobuild
Thomas C. Terwilliger
terwilliger at lanl.gov
Wed Mar 23 13:02:42 PDT 2011
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
>> ======================
>> _______________________________________________
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>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
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