[phenixbb] TLS makes my r-factors shoot through the roof

Pavel Afonine pafonine at lbl.gov
Wed May 30 02:56:37 PDT 2012

Hi Morten,

sorry for the trouble once again.

Hm.. this seems like a case where I need the data to be able to 
reproduce the problem myself and fix it. Could you please send me all 
inputs so I can do it? I'll need data and model, and tell what exactly 
did you do, or just .eff file. Please send files off-list: directly to 
my email.

I'm traveling right now so I might not be able to look right away, 
though I will do my best to address this problem asap (once I get the 


On 5/29/12 7:39 AM, Morten Groftehauge wrote:
> I like the new version but it does not seem to have helped much. 
> Before it shot up by 3%, this time by 2.5%.
>     On 29 May 2012 12:23, Pavel Afonine <pafonine at lbl.gov
>     <mailto:pafonine at lbl.gov>> wrote:
>         Hi Morten,
>         I'm sorry about the problem.
>         Are you using the latest Phenix? There was a bug in
>         phenix.refine that I fixed a while ago, and the bug behavior
>         was very similar to what I see happening in your case.
>         Could you please try the latest version and see if the problem
>         goes away? Please let me know.
>         Pavel
>         On 5/29/12 3:56 AM, Morten Groftehauge wrote:
>             Hi Phenixbb,
>             3.2A data, 110 Wilson B, I41, twinned. Imperfect inverted
>             repeat dsDNA with 4 protein monomers, NCS not used in
>             refinement.
>             If I don't include TLS I get a nice stable R-factor while
>             RMS goes down.
>             If I include TLS (whether as one group per chain or as
>             chosen by Phenix) this happens:
>             Density disappears around some of the DNA bases as an
>             obvious difference. If I run Refmac with TLS it just never
>             finishes.
>             While I could just refine without TLS this does make me
>             worried that there is something wrong with my model or my
>             data (besides being terrible).
>             Cheers,
>             Morten

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