[phenixbb] TLS makes my r-factors shoot through the roof
pafonine at lbl.gov
Wed May 30 02:56:37 PDT 2012
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
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.
> 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
> 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
> 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).
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