[phenixbb] adding hydrogens -> increasing clash score

Tatyana Sysoeva tatyanasysoeva at gmail.com
Sat Jul 30 11:35:21 PDT 2011

I ran the same commands with the build dev-833.
Below are the results.
These parameters are obtained by running phenix.ramalyze, cbetdev, and
I am almost done repeating fix-rotamers run. First time it gave a way worse
validation results then before running phenix without fix_rotamers=true.
I don't understand what I am doing wrong in the runs and would appreciate
your help!


I used phenix-dev-833 to test the riding hydrogens refinement at 3.6A.

I ran two indentical commands:

Command line arguments: "model.pdb" "data.mtz" "main.ncs=true"
"ncs.find_automatically=false" "ncs_groups.params"
"refinement.input.xray_data.high_resolution=3.6" "mgadpbef.cif"

 with the only difference in the input files – ncs.params and model.pdb

Model pdb contained the model identical to the control run but with added H
atoms. I have not add H to the ADP molecules since I did not know how to
write a correct CIF file for it. NCS definitions were changed by addition of
“and not (element H)” to each line. It was done to exclude H from the NCS

*no hydrogens*

*with hydrogens*

# Date 2011-07-29 Time 19:09:58 EDT -0400 (1311980998.46 s)

wall clock time: 2646.75 s

Start R-work = 0.2891, R-free = 0.3267

Final R-work = 0.2868, R-free = 0.3304

# Date 2011-07-29 Time 20:14:20 EDT -0400 (1311984860.16 s)

wall clock time: 6517.60 s

Start R-work = 0.2910, R-free = 0.3273

Final R-work = 0.2720, R-free = 0.3353

clashscore 31.77

clashscore 96.12

cbeta 0

cbeta 151

rama 12.62% outliers

rama 19.67% outliers

Interestingly in previous release version the same refinement runs produced:

without H clashscore = 77.580195/cbeta =8
with H clashscore = 119.729960/cbeta=330
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