[phenixbb] adding hydrogens -> increasing clash score

[Pavel Afonine]

Hi Tatyana,

could you please send me the data and model files (off-list) so I can 
investigate? I will post the summary on phenixbb once we know what's 
going on.

I see a number of potential issues but I don't want to waste time 
guessing, since it's much more efficient if you send me the files then I 
run some tests and tell you how to proceed.

I'm pretty confident there is a quick fix.

Thanks!
Pavel.

On 7/30/11 11:35 AM, Tatyana Sysoeva wrote:
> I ran the same commands with the build dev-833.
> Below are the results.
> These parameters are obtained by running phenix.ramalyze, cbetdev, and 
> clashscore.
> 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!
>
> Thanks,
> Tanya
>
>
> 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" 
> "refinement.ncs.excessive_distance_limit=None" 
> "strategy=individual_sites+individual_sites_real_space+group_adp+occupancies"
>
> 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 groups.
>
> _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
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20110731/df1a0ede/attachment-0001.htm>