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Refinement and glycosylation.
by Jan van Agthoven 12 Dec '12

12 Dec '12

Hi everyone, I refined my structure using phenix.refine and used the following parameters to define the ASN-NAG link: refinement.pdb_interpretation.apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resseq x residue_selection_2 = chain A and resname ASN and resseq y } However I would like the glycosylation to be Beta (NAG in Beta configuration). How can I define this in the parameter file? Thanks,

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pathological case with soaking
by Appu kumar 12 Dec '12

12 Dec '12

Respected members,, I have one question regarding soaking. Binding of the substrate to enzyme leads to active site closure. So if we are soaking the enzyme crystal with the substrate, and collecting the data and solving the structure, then how would one distinguish the existence of apo and substrate bound form of enzyme in same crystal. I meant to say, soaking may cause the crystal to have quasi-apo-enzyme and quasi-substrate-enzyme complex existing together. Is there any way to take care of such pathological condition during data processing, or structure solving? . I would highly appreciate your help and looking forward to get valuable advices. Please graduate me in this kind of weired situation. Thank you Appu

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Re: [phenixbb] phenix and weak data
by Douglas Theobald 12 Dec '12

12 Dec '12

Hi Ed, Thanks for all the info, its very useful. So I have two questions now. What is the evidence, if any, that the exptl sigmas are actually negligible compared to fit beta (is it alluded to in Lunin 2002)? Is there somewhere in phenix output I can verify this myself? And, in comparison, how does refmac handle the exptl sigmas? Maybe this last question is more appropriate for ccp4bb, but contrasting with phenix would be helpful for me. I know there's a box, checked by default, "Use exptl sigmas to weight Xray terms". Cheers, D On Dec 10, 2012, at 1:04 PM, Ed Pozharski <epozh001(a)UMARYLAND.EDU> wrote: > On 12/06/2012 05:35 PM, Douglas Theobald wrote: > >> However, I was surprised to hear rumors that with phenix "the data are not properly weighted in refinement by incorporating observed sigmas" and such. > Douglas, > > Up to a certain point in its derivation, maximum likelihood target is > exactly the same in all implementations. Where Lunin/cctbx/phenix > approach is different is that it derives analytical expressions for > model error parameters by optimization of the maximum likelihood target > itself with respect to these. It's a clever approach, except that it > does not work unless one ignores experimental errors. > > A minimization target contains essentially a difference between > calculated and observed structural amplitudes (properly scaled etc). > For each reflection it must be properly weighted by combined > uncertainty, which includes both model error and experimental error. > Assume that former is much larger than the latter which can then be > ignored. Both errors are now combined in a single parameter (per > resolution shell, called beta), which can be calculated analytically. > Once this is done, we go back and check - and indeed, this combined > model error is larger than the experimental one. > > There are few interesting consequences of this. > > First, it seems clear that weighting every reflection in a resolution > shell the same way is a compromise. One expects less precisely measured > reflections should be weighted down. But the effect may be small. > > Second, mathematically it turns out that the target value (towards which > Fc is pushed) for some reflections should be set to exactly zero. The > cutoff is Fo<sqrt(es*beta). Quote from Lunin et al., 2002: > > "...in this case, the likelihood-based target fits the calculated > magnitude to the zero value (Fs*=0) regardless of the particular value > of Fobs." > > Third, one is tempted to interpret the beta parameter as the model > variance. The problem is sqrt(beta) ends up significantly higher than > one would expect from the R-values. This, imho, poses a bit of a problem > in light of the second issue - resetting Fs* to zero for "weak > reflections". If beta ends up overestimated for whatever reason, then > those reflections aren't that weak anymore. > > Yet, the refinement still seems to work just fine. So perhaps > overestimated model error is not a big deal in that respect. Indeed it > is not. In fact, one can multiply beta by arbitrary number, and the > relative weight applied to individual reflections in maximum likelihood > will remain roughly the same. So while it provides robust > resolution-dependent weighting, the absolute value of beta parameter is > not easily interpreted (as absolute model error). > > Hopefully all is well in sunny Waltham, > > Ed. > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs > >

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Postdoctoral position in crystallography of the CFTR ion channel
by Machius, Mischa Christian 12 Dec '12

12 Dec '12

On behalf of a collaborator, I'd like to bring this open position to your attention. Postdoctoral position available in the laboratory of Jack Riordan, Dept of Biochemistry and Biophysics and Cystic Fibrosis Center, University of North Carolina at Chapel Hill. To join and provide a major contribution to a team working on the production, purification and characterization of the CFTR ion channel protein for crystallization and X-ray crystallography. Required experience working with membrane proteins and lipids and/or protein crystallization. Focus will be on crystallization in meso in collaboration with experts in that technology. Contact: jack_riordan(a)med.unc.edu<mailto:[email protected]> The University of North Carolina is an equal opportunity employer. ----------------------------------------------------------------------- Mischa Machius, PhD Director, Center for Structural Biology Assoc. Professor, Dept. of Pharmacology University of North Carolina 4079 Genetic Medicine CB#7365 120 Mason Farm Road Chapel Hill, NC 27599-7365, U.S.A. tel: +1-919-843-4485 fax: +1-919-966-5640 email: machius(a)med.unc.edu<mailto:[email protected]>

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SA Fo-Fc omit map
by Mengbin Chen 12 Dec '12

12 Dec '12

Dear Phenix Users, I have been playing around with Phenix AutoBuild GUI to generate a fo-fc sa omit map of the ligand in a protein structure, and I have the input files as follows: output.mtz (data type:experimental data) ligand.pdb (data type: omit box atoms & ligands) ligand.cif (data type: restraints of the ligand) protein.pdb (data type: starting model) omit map type: simulated annealing omit region: omit around PDB fie I have set the occupancies of all ligand atoms zero and deleted the ligand coordinates in my starting model. After the run finished and I checked the refined coordinates and map.mtz in COOT, I found that there was no electron density around the ligand while the protein model was in electron density, which was exactly opposite of what I wanted before. Furthermore, I have 3 Mg2+ ions in protein.pdb file, all of which moved away from where they were after the refinement run, which was not wanted either. Could anyone tell me how to do the sa omit map of ligand correctly? Thanks in advance! Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

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Re: [phenixbb] Fwd: parameters for averaged kick maps
by Pavel Afonine 11 Dec '12

11 Dec '12

Hi Jose, kick-map related parameters in ordered_solvent scope of parameters are leftover that I forgot to remove back when I was working on it. So you can see it as a minor bug. And yes, you can't change them. Sorry about delayed answer (I saw the email on phenixbb but did note reply immediately and it sank in the flood of other stuff). Pavel On 12/10/12 11:04 AM, Jose M de Pereda wrote: > Dear Phenix Team, > > Last week I sent an e-mail to the phenixbb regarding the parameters > that control de generation of averaged kick maps. Unfortunately, I > have not received any feedback from the community. > > I wonder if you could give me some help on this subject. > > Probably, the calculation of averaged kick maps is already very well > optimized in phenix.refine and phenix.maps. Yet, I am still curious. > > Thanks a lot in advance > All the best > > Jose > > > -------- Original Message -------- > Subject: [phenixbb] parameters for averaged kick maps > Date: Tue, 04 Dec 2012 10:12:46 +0100 > From: Jose M de Pereda <pereda(a)usal.es> > Reply-To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > > > > Dear all, > > I would like to compare averaged kick maps obtained using different “kick sizes”. > Is it possible to define the kick size and the number of kicks in phenix.refine and/or phenix.maps? > > In phenix.refine, the “ordered_solvent” section has keywords to control the generation of kick maps: > kick_map { > kick_size = 0.5 > number_of_kicks = 100 > } > But, it seems to me that these can not be used during the generation of maps or maps’ coefficients. > > Related with this issue, does phenix.refine always use the same kick > size or does it adjust it ad hoc (e.g. based on ML error estimates)? > > Thanks a lot, > Jose > > > -- > ------------------------------------------------------------ > Jose M de Pereda, PhD > Instituto de Biologia Molecular y Celular del Cancer (IBMCC) > Spanish National Research Council - University of Salamanca > Campus Unamuno s/n > E-37007 Salamanca, Spain > Phone: +34-923-294817 > Fax: +34-923-294795 > http://xtal.cicancer.org/ > ------------------------------------------------------------ > >

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Simulated annealing map
by Appu kumar 10 Dec '12

10 Dec '12

Thank you Terwilliger, Thomas for you quick reply, for guiding me on how to make simulated annealing omit map. Now i am able to make it but i have one question. i want to show the SA omit map of ligand with the map of omitted region around ligand. I tried it, i got the map also, but the omitted map of region around ligand is show in recatangular box which is not as great as of ligand inside the omitted region. Thank you

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Please apply for RapiData 2013, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 10 Dec '12

10 Dec '12

We are offering RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Real Space CC Raw Data
by Eddie Pryor 08 Dec '12

08 Dec '12

Hi, All, To satisfy a reviewer, I would like to include a supplemental figure that contains, among other things, Real Space CC for each residue. I was wondering where this raw data might be stored so that I can parse and create a graph with it. The only thing I could find was in the Refine_###_info.txt log file, but that only included values less than 0.7. I know that all of the residues / CC values can be listed through the GUI, but with ~900 residues in my ASU, this is something I do not want to do manually! Thanks! --Eddie Pryor

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How to make simmulated annealing omit map
by Appu kumar 07 Dec '12

07 Dec '12

Dear Users, I am refining a enzyme structure with ligand. I want to make the simulated annealing omit map of ligand including with 4 Angestron radius around the ligand. I am seeking your valuable advice to help me out. I know how to make omit map but i have not come accross making simmulated annealing omit map. I would appreciate your help. Thank you Appu

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