I just tried the latest cci_apps and re-ran the refine job. The new version seems to clear up the problem. <br><br>Thanks,<br><br>Mary<br><br><div class="gmail_quote">On Feb 1, 2008 4:05 PM, Peter Zwart <<a href="mailto:PHZwart@lbl.gov">PHZwart@lbl.gov</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Mary,<br><br>Can you try and download the latest cci_apps and recompute the maps<br>with phenix.refine?<br>
I did make some updates since rc6 in the dewtinning code.<br><br>Cheers<br><div><div></div><div class="Wj3C7c"><br>Peter<br><br><br><br><br>2008/2/1, Mary Fitzgerald <<a href="mailto:mary.x.fitzgerald@gmail.com">mary.x.fitzgerald@gmail.com</a>>:<br>
> Peter-<br>> I've attached an image from coot. I loaded my model and then a cns<br>> detwinned 3fo-2fc map (purple) and the 2fo-fc (blue) from phenix both are<br>> contoured at 1.5. The 3fo-2fc is the only map have at the moment equivalent<br>
> to the 2fo-fc model although it had waters in the model. I have the<br>> symmetry brought up and there's not a symmetry related molecule in the area.<br>> I've been working with this model quite a while and have never seen density<br>
> there before. It shows up in a couple of other spots as well with nothing<br>> appearing in the fo-fc maps, which I didn't show here. It looks as if I'm<br>> missing part of my model in areas that there shouldn't be any model.<br>
><br>> Thanks,<br>> Mary<br>><br>><br>> On Feb 1, 2008 2:59 PM, Peter Zwart <<a href="mailto:PHZwart@lbl.gov">PHZwart@lbl.gov</a>> wrote:<br>> > Can you send a picture of the density and/or the data and model so I<br>
> > can have a look.<br>> > The detwinning is done differently and for twin fractions of 0.5<br>> > something weird mihgt be happening.<br>> ><br>> > Thanks<br>> ><br>> > Peter<br>
> ><br>> ><br>> ><br>> ><br>> > 2008/2/1, Mary Fitzgerald <<a href="mailto:mary.x.fitzgerald@gmail.com">mary.x.fitzgerald@gmail.com</a>>:<br>> ><br>> ><br>> ><br>> > > I'm new to phenix and just installed Phenix 1.3 beta rc6.<br>
> > ><br>> > > I've taken a data set that I've been refining in cns and am trying<br>> > > phenix.refine. The data has a twinning fraction of 0.5. I'm seeing<br>> what I<br>> > > think is odd in the 2mFobs-DFmodel.map. If I'm reading the<br>
> documentation<br>> > > correctly, this map should be detwinned (I also set<br>> > ><br>> refinement.twinning.detwin.map_types.aniso_correct=true), I<br>> > > see alot of extra density where there is no model, nor a symmetry<br>
> related<br>> > > molecule in coot. I don't see this extra density in my detwinned 2fofc<br>> cns<br>> > > maps.<br>> > ><br>> > > So, could the extra density I'm seeing be due to using a different<br>
> program<br>> > > and it is detwinning the data differently. The extra density is from<br>> the<br>> > > twin????<br>> > ><br>> > > Any input would be appreciated,<br>> > ><br>
> > > Mary X. Fitzgerald<br>> > > Postdoctoral Associate<br>> > > Arnold Lab<br>> > ><br>> > ><br>> > > _______________________________________________<br>> > > phenixbb mailing list<br>
> > > <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>> > > <a href="http://www.phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br>
> > ><br>> > ><br>> ><br>><br>><br>><br></div></div></blockquote></div><br>