May 2012 - phenixbb - phenix-online.org

Re: [phenixbb] Geometry Restraints - Anisotropic truncation
by Frank von Delft 02 May '12

02 May '12

Hi Pavel > we discussed this with Randy the other day.. A couple of copy-pasts from > that discussion: > > In general, given highly anisotropic data set: > > 1) maps calculated using all (unmodified) data by phenix.refine, > phenix.maps and similar tools are better than maps calculated using > anisotropy truncated data. So, yes, for the purpose of map calculation > there is no need to do anything: Phenix map calculation tools deal with > anisotropy very well. How did you define "better"? If there are a lot of reflections without signal, that makes them essentially missing, so by including them, you're effectively filling in for those reflections with only DFc. If anisotropy is very strong (i.e. many missing reflections), does that not introduce very significant model bias? The maps would look cleaner, though. (I haven't tested myself, btw; I'm genuinely wondering.) > 2) phenix.refine refinement may fail if one uses original anisotropic > data set. This is probably because the ML target does not use > experimental sigmas (and anisotropy correction by UCLA server is nothing > but Miller index dependent removing the data by sigma criterion - yeah, > that old well criticized practice of throwing away the data that you > worked hard to measure!). May be using sigmas in ML calculation could > solve the problem but that has to be proved. If there are large swathes of reciprocal space without signal - I don't see why shouldn't that be excluded? Tossing out individual reflections is of course silly, but what's wrong with trimming down the edges of the elipsoid? Cheers phx

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Inputting DNA for Phenix MR and/or Autobuild
by Charles Allerston 02 May '12

02 May '12

Dear all, I can't find much in the way of documentation for this. Can someone point me to some please? I basically want to know the correct format for entering DNA into the search for MR and inputting into Autobuild. If I have a double stranded DNA do I enter it as >DNA1 AATT:AATT >DNA1 AATT TTAA etc. ? cheers, charlie Dr. Charles Allerston Genome Integrity & Repair Structural Genomics Consortium Nuffield Department of Medicine Old Road Campus University of Oxford OX3 7DQ http://www.thesgc.org/scientists/groups/oxford/genome-integrity-and-repair

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Call for submissions to June 2012 Computational Crystallography Newsletter (CCN)
by Nigel Moriarty 01 May '12

01 May '12

Calling for articles and short communications of interest to structural biologists. The deadline for publication in the June 2012 issue is 29 May, 2012. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and the template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Estimation of ligand binding affinity by occupancy refinement
by Zoran Stefanic 01 May '12

01 May '12

Dear all, I have a question about sensitivity of occupancy refinement in phenix. I have a series of datasets done at our home instrument of relatively modest resolutions from 2.8 to 3 A. These are performed on crystals soaked in progressively higher ligand concentrations. We are trying to see to which of the several active sites the ligand binds first so we went from low to high ligand concentrations. We wanted to estimate the amount of ligand bound by refining the occupancies of the ligand. We expect one active site to bind more strongly than the other two active sites. This was indeed what we observed but when we refine the occupancies of the ligands in weaker binding sites starting at 0.2 occupancies they rise to 0.5-0.6 although some atoms are totally out of density and some are in. B factors are reasonable, i.e. don't go wild. My question would be: how reliable is this estimation of ligand binding by occupancy refinement? Why doesn't the occupancy of ligands stay low if afterwards the density fit of the ligand looks rather unconvincing? Thank you in advance Zoran -- Dr. Zoran Stefanic Division of Physical Chemistry Rudjer Boskovic Institute Bijenicka 54 P.O. Box 180 Zagreb Croatia Phone: 00 385 1 457 1203 Fax: 00 385 1 468 0245

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