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Hi Morten,<br>
<br>
sorry for the trouble once again.<br>
<br>
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.<br>
<br>
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 files).<br>
<br>
Thanks,<br>
Pavel<br>
<br>
On 5/29/12 7:39 AM, Morten Groftehauge wrote:
<blockquote
cite="mid:CAEAG6YS1kzbg9-y1g2qkv=q_bC2v+y2=cgYPbsx-Q6AcV9L2kA@mail.gmail.com"
type="cite">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%.
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<div class="h5"><br>
<br>
<div class="gmail_quote">On 29 May 2012 12:23, Pavel
Afonine <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi
Morten,<br>
<br>
I'm sorry about the problem.<br>
<br>
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.<br>
<br>
Could you please try the latest version and see if
the problem goes away? Please let me know.<br>
<br>
Pavel
<div><br>
<br>
On 5/29/12 3:56 AM, Morten Groftehauge wrote:<br>
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Hi Phenixbb,<br>
<br>
3.2A data, 110 Wilson B, I41, twinned.
Imperfect inverted repeat dsDNA with 4 protein
monomers, NCS not used in refinement.<br>
If I don't include TLS I get a nice stable
R-factor while RMS goes down.<br>
If I include TLS (whether as one group per
chain or as chosen by Phenix) this happens:<br>
<br>
<br>
<br>
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Density disappears around some of the DNA
bases as an obvious difference. If I run
Refmac with TLS it just never finishes.<br>
<br>
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).<br>
<br>
Cheers,<br>
Morten<br>
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