[phenixbb] Worse R factor with newer version of phenix

Jan van Agthoven janccp4 at gmail.com
Tue Oct 8 08:50:19 PDT 2013


I sent you the files. To answer your question, I had weight
optimization. Surprisingly, it worked well with phenix 1.8.2. But I'm
ready to believe that there is a bug in my data (maybe not tolerated
by this version of phenix)
Thanks


2013/10/8, Nathaniel Echols <nechols at lbl.gov>:
> Whenever you see the bond and angle RMSDs blow up like this, it means that
> the weight between the X-ray and geometry restraint terms was not
> calculated correctly.  Probably the quickest solution is to set wxc_scale
> much lower - the default is 0.5 but at this resolution I think 0.1 would be
> more appropriate, and you could try setting it even lower.  (Note that if
> you have weight optimization turned on this will have no effect.)  However,
> the fact that you didn't see this before suggests that there may be a bug
> somewhere that is specific to your data.  Could you please send us input
> files and log file at bugs at phenix-online.org so one of us can take a look?
>  (These will be kept private, obviously.)
>
> thanks,
> Nat
>
>
> On Mon, Oct 7, 2013 at 12:46 PM, Jan van Agthoven <janccp4 at gmail.com>
> wrote:
>
>> Hi everyone,
>> I've been working on a low resolution structure (3.6A) which was
>> previously refined with phenix  1.8_1069 (with a reference model,
>> strategy=individual_sites,individual_adp ). I used the same input
>> files and parameters and ended up with significantly different R
>> factors.
>>
>> Start: r_work = 0.2850 r_free = 0.3189 bonds = 0.005 angles = 1.059
>>
>> Final: r_work = 0.2609 r_free = 0.3160 bonds = 0.003 angles = 0.997
>>
>> For the old version
>>
>> and
>>
>> Start: r_work = 0.2779 r_free = 0.3183 bonds = 0.006 angles = 1.141
>> Final: r_work = 0.2889 r_free = 0.3303 bonds = 0.021 angles = 2.737
>>
>> with the new  version 1.8.4
>>
>> Remarkably it also came with an increased number of C-beta deviation
>> (0 against 16!).
>>
>> Adding tls refinement or ramachandran restrains did not help.
>>
>> Now because I was using the .eff file of an old version of phenix, it
>> came with a long list of unused parameters. These parameters however
>> were all used by default.
>>
>> What should I do? Should I go back to this old phenix, or is there a
>> way to improve the result?
>>
>> Thanks,
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>


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