<div dir="ltr">Here is the problem:<div><br></div><div>phenix.mtz.dump resolve_1_190_phenix.mtz</div><div>...</div><div><div> HLA xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman)</div>
<div> HLB xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman)</div><div> HLC xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman)</div>
<div> HLD xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman)</div></div><div><br></div><div>We ignore arrays with all zeros, since they're obviously not correct - however, the feedback given to the user is deficient. I am open to suggestions about how we can improve this, but I am reluctant to assault users with pop-ups every time bogus information is detected, especially since this will increase the latency of the GUI.</div>
<div><br></div><div>The file from AutoSol you should actually use is probably named overall_best_refine_data.mtz, which contains the original, purely experimental phases (along with data and R-free flags, of course). We don't recommend using the density-modified phases as restraints. (I am not sure why Resolve would output all zeros; that is a question for Tom. I did however notice the same thing in a file generated by AutoSol for a tutorial dataset.)</div>
<div><br></div><div>-Nat</div><div><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, May 12, 2014 at 8:21 AM, Jonathan Grimes <span dir="ltr"><<a href="mailto:jonathan@strubi.ox.ac.uk" target="_blank">jonathan@strubi.ox.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
hi nat<br>
<br>
i created this mtz file.....by taking a resolve.mtz<br>
and putting it back thru phenix.<br>
<br>
from the GUI and from the command line phenix<br>
doesnt like my HLs coeffs.<br>
<div class="im HOEnZb"><br>
thanks<br>
jon<br>
<br>
Dr. Jonathan M. Grimes,<br>
</div><div class="im HOEnZb">NDM Senior Reseach Fellow Diamond Research Fellow<br>
University Research Lecturer Diamond Light Source<br>
Division of Structural Biology Diamond House<br>
Wellcome Trust Centre for Human Genetics Harwell Science Campus<br>
University of Oxford Didcot<br>
Roosevelt Drive, OX11 0DE<br>
Oxford OX3 7BN, UK<br>
<br>
Email: <a href="mailto:Jonathan@strubi.ox.ac.uk">Jonathan@strubi.ox.ac.uk</a>, Web: <a href="http://www.strubi.ox.ac.uk" target="_blank">www.strubi.ox.ac.uk</a><br>
Tel: <a href="tel:%28%2B44%29%20-%201865%20-%20287561" value="+441865287561">(+44) - 1865 - 287561</a>, FAX: <a href="tel:%28%2B44%29%20-%201865%20-%20287547" value="+441865287547">(+44) - 1865 - 287547</a><br>
<br>
<br>
<br>
---- Original message ----<br>
</div><div class="HOEnZb"><div class="h5">>Date: Mon, 12 May 2014 07:44:14 -0700<br>
>From: Nathaniel Echols <<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>><br>
>Subject: Re: [phenixbb] HLs not recognised<br>
>To: Jonathan Grimes <<a href="mailto:jonathan@strubi.ox.ac.uk">jonathan@strubi.ox.ac.uk</a>><br>
>Cc: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>
><br>
> This is a little strange - the GUI should not be<br>
> allowing you to select an array that won't work for<br>
> refinement. Could you please send me (off-list!)<br>
> both MTZ files that you tried using? (I don't<br>
> think I need data or anything else for this.)<br>
> thanks,<br>
> Nat<br>
><br>
> On Mon, May 12, 2014 at 5:49 AM, Jonathan Grimes<br>
> <<a href="mailto:jonathan@strubi.ox.ac.uk">jonathan@strubi.ox.ac.uk</a>> wrote:<br>
><br>
> i have now used phenix to read in the mtz file,<br>
> read all the arrays<br>
> and make a new mtz file.<br>
><br>
> phenix recognised the HLs as Hend/latt coeffs.<br>
><br>
> i used the eff file to run phenix.refine at the<br>
> command line<br>
> and got this error<br>
><br>
> Not a suitable array of experimental phases:<br>
> refinement.input.experimental_phases.labels=HLA,HLB,HLC,HL<br>
><br>
> The phases were orginally derived by Phenix<br>
> using the auto solve GUI.<br>
> Jon<br>
><br>
> Dr. Jonathan M. Grimes,<br>
> NDM Senior Reseach Fellow <br>
> Diamond Research Fellow<br>
> University Research Lecturer <br>
> Diamond Light Source<br>
> Division of Structural Biology <br>
> Diamond House<br>
> Wellcome Trust Centre for Human Genetics <br>
> Harwell Science Campus<br>
> University of Oxford <br>
> Didcot<br>
> Roosevelt Drive, <br>
> OX11 0DE<br>
> Oxford OX3 7BN, UK<br>
><br>
> Email: <a href="mailto:Jonathan@strubi.ox.ac.uk">Jonathan@strubi.ox.ac.uk</a>, Web:<br>
> <a href="http://www.strubi.ox.ac.uk" target="_blank">www.strubi.ox.ac.uk</a><br>
> Tel: <a href="tel:%28%2B44%29%20-%201865%20-%20287561" value="+441865287561">(+44) - 1865 - 287561</a>, FAX: (+44) - 1865 -<br>
> 287547<br>
><br>
> ---- Original message ----<br>
> >Date: Mon, 12 May 2014 11:32:39 +0100<br>
> >From: <a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a> (on<br>
> behalf of Jonathan Grimes<br>
> <<a href="mailto:jonathan@strubi.ox.ac.uk">jonathan@strubi.ox.ac.uk</a>>)<br>
> >Subject: [phenixbb] HLs not recognised<br>
> >To: <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
> ><br>
> ><br>
> > I am trying to refine a structure at low<br>
> resolution and would like to<br>
> > use phase restraints. using the GUI even<br>
> though HLs are present<br>
> > in the MTZ file, and are type<br>
> “A”…checked with CAD…..i am not given<br>
> > the option of selecting them.<br>
> ><br>
> > not clear to me what I’m doing wrong.<br>
> ><br>
> > hints most wellcome<br>
> > thanks<br>
> > jon<br>
> ><br>
> ><br>
> >Dr. Jonathan M. Grimes,<br>
> >NDM Senior Reseach Fellow<br>
> >University Research Lecturer<br>
> >DIAMOND Research Fellow<br>
> ><br>
> >Division of Structural Biology<br>
> >Wellcome Trust Centre for Human Genetics<br>
> >University of Oxford<br>
> >Roosevelt Drive,<br>
> >Oxford OX3 7BN, UK<br>
> ><br>
> >Email: <a href="mailto:Jonathan@strubi.ox.ac.uk">Jonathan@strubi.ox.ac.uk</a>, Web:<br>
> <a href="http://www.strubi.ox.ac.uk" target="_blank">www.strubi.ox.ac.uk</a><br>
> >Tel: <a href="tel:%28%2B44%29%20-%201865%20-%20287561" value="+441865287561">(+44) - 1865 - 287561</a>, FAX: (+44) - 1865 -<br>
> 287547<br>
> ><br>
> >_______________________________________________<br>
> >phenixbb mailing list<br>
> ><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
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</div></div></blockquote></div><br></div></div>