Search results for "look through"

Re: [phenixbb] Fw: Strange behaviour of phenix.maps fill_missing_f_obs

by Pavel Afonine

Hi Tristan, in recent Phenix versions we replaced "kick map" option with a generalized (and more sophisticated) concept that we call FEM - Feature Enhanced Map. The paper is scheduled to appear in Acta D: http://journals.iucr.org/d/services/readerservices.html Meanwhile you can read through the set of pages that explain the concept and show examples: http://www.phenix-online.org/presentations/fem_06MAY2014.pdf Let me know if you have questions! Pavel On 2/5/15 1:12 AM, Tristan Croll wrote: > > My previous email was hung up in moderation due to my attaching a jpeg > that tripped the size limit. In any case, I've done a bit more testing > and the problem doesn't actually originate in the fill_missing_f_obs, > but in the kicked map algorithm. If, as per the attached parameter > file, I have a kicked map in the to-do list, every map past that point > is garbled (the kicked map itself appears fine). Set kicked to False, > and all maps come out looking normal. > > > I should also note that the sharpening_b_factor parameter seems > inverted from the normal convention: a negative value gives smoothing > rather than sharpening. > > > Cheers, > > > Tristan > > ------------------------------------------------------------------------ > *From:* Tristan Croll > *Sent:* Thursday, 5 February 2015 3:47 PM > *To:* phenixbb(a)phenix-online.org > *Subject:* Strange behaviour of phenix.maps fill_missing_f_obs > > Hi, > > > I'm working on a package that makes scripted calls to phenix.refine to > generate a series of ccp4 formatted maps, and have run into an odd > problem. Using the attached parameter file I get a series of perfectly > normal-looking maps, except in the case of the filled 2mFo-DFc map > (test-3_2mFo-DFc_fill.ccp4 - the second-last map generated). This > comes out as a series of disconnected blobs (it looks rather like a > mFo-DFc map, but it doesn't match the actual mFo-DFc > map). When I take the resulting .mtz file and generate the filled map > in Coot (with or without omission of Rfree flags), on the other > hand, it seems to come out fine. There are no error messages in the > log, but I suspect the default method to fill in the missing F_obs > may be returning /only/ the missing F_obs? > > > I've attached a small example image. Red wireframe is the 2mFo-DFc > unfilled map at 1 sigma; green translucent is the 2mFo-DFc filled map > at 1 sigma; yellow is the mFo-DFc map at 2 sigma. > > > The test structure I'm using is nothing special: 3WSY, picked > more-or-less at random off the protein data bank. Phenix version is > 1.9.1692, installed in Fedora 21. > > > Have I done something wrong that I'm just not seeing, or is there a > bug here? > > > Thanks, > > > Tristan > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

10 years, 4 months

Re: [phenixbb] questions about twinned structure and MR

by Peter Zwart

Hi Christina, > I am new to Phenix and am facing my first twinned structure. While I wait > for my copy of Yeates Methods in Enzymology (albeit from 1997) to be > delivered, perhaps this bb could answer a few questions? There are a number of excellent papers besides the one you mention. Check for instance Dauter, Z. (2003). Acta Cryst. D59, 2004-2016. Parsons, S. (2003). Acta Cryst. D59, 1995-2003. Zwart,Lebedev, Mushudov,Adams Acta Cryst. (2008). D64, 99-107 > At what point do I detwin, or do I not do it at all? It seems Phenix does > this itself, on the fly? Is it refining the twin fraction too? No need to detwin really. Maybe helpfull for density modification, but typically it does more harm then good. phenix.refine does refin ethe twin fraction as well indeed. Please provide data as obtained from your data reduction program without detwinning it yourself. > MR (Phaser) finds solutions with twinned or detwinned data. However, the > solutions vary by 180degrees, so I suspect I'm finding solutions for both > h,k,l and h,-k,-l. Quite possible. > These come from two different runs, but one has refined > LLgain of 1010.8 (matches soln found with detwinned data, both run through > ccp4), and other has refined LLgain of 1073 (through Phenix; it's rotated > 180degrees from the other). How many copies do you have in the ASU? > When performing AutoBuild after AutoMR, should I worry that I haven't > assigned Rfree? Does Phenix account for twinning when it does this > automatically, or what keyword(s) do I need to include? It should assign free flags automatically in a sensible manner when using the autobuild wizard. Please provide the wizard with a set of parameters so that it knows that your data is twinned. It will use that in refinement, but not in density modification. > I see a section in the documentation about refining twinned structures, and > am looking forward to getting to that point! I just want to be sure I'm > following a "correct" procedure for the steps leading up to that. From the > literature, it seems quite common to not account for twinning until > refinement. My concern is the two MR solns...which should I use? If I know > it's twinned, shouldn't I account for that from the beginning? Just pick the best one. If you pick the 'twin related solution' your twin fraction could refine to a value larger than 0.5. > More details: > P41, data good to 2.2A, 2 molecules in the AU, twinning fraction ~0.4. > Rmerge from scaling is reasonable at ~11% overall. MR model is 100% > identical to this data, but from a different spacegroup (thus I'm running > MR). > > Thanks for any tips or guidance! > Christina Bourne The dimer in the ASU is probably the reason why you pick up two possible solutions. The dimer NCS axis is most likely parallel to the twin axis (two fold along a). So in this case, the twin related solution and NCS related solution might be the same. The twin tutorial in the phenix documentation should provide some useful info. HTH Peter

17 years, 2 months

Re: [phenixbb] Gap between R and Rfree

by Kendall Nettles

Did you check your data Kendall On Feb 25, 2010, at 12:43 PM, "Young-Jin Cho" <yjcho(a)brandeis.edu> wrote: > > Thanks for your suggestions, Phill. > When I did Ramachandran analysis, it shows 96.60% in preferred > region and 2.62% in allowed regions, and 0.79% is in outlier. > Geometry looks Ok. I also did optimize_wxc and optimize_wxu, and tls > option. it didn't help much. > Now I am trying to scale down. > > Thanks again. > > Young-Jin > > > 0. Use Molprobity or the Validation tools in Coot to look at your > structure and see what errors you can fix. > 1. What is your geometry like ? Try reducing wxc_scale (try > wxc_scale=0.5) and see what happens. > 2. What is the variation of B-factors across bonds ? Try reducing > wxu_scale - perhaps wxu_scale=0.5 or less. > 2a. phenix.refine is autocratic about wxu_scale if you're using TLS > so > setting it yourself does not help. > 3. Since R-free of 0.298 is a little high for a 2.5 Angstrom > structure, > you should carefully check your model. Perhaps you have a high > proportion of disordered structure, which can cause this. If you feel > that your model is correct, you could explore using TLS on your model. > Potential TLS groups can be found using the TLSMD server at: > http://skuld.bmsc.washington.edu/~tlsmd/ although the results should > always be filtered through a common-sense definition of domain/group > boundaries (e.g. don't break in the middle of helices unless there's a > good reason to). > > Phil Jeffrey > Princeton > > > Young-Jin Cho wrote: >> Hi everyone, >> I recently got a diffraction data and am trying to refine it. The >> question is whatever I did the gap between R and Rfree stay far >> away: .2140/.2982 around 2.5 A resolution. (water added and >> isotropic(individual_adp) and so on). >> Although I am redoing with many different approaches, if anyone can >> give me any comments or suggestions, it would be helpful. >> >> Thanks in advance, >> >> Young-Jin > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > > -- > Postdoctoral Fellow, Kern Lab > Biochemistry Department/HHMI > Brandeis University > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

15 years, 4 months

Re: [phenixbb] Changing an amino acid to an unusual amino acid

by Nigel Moriarty

Natalia I have attached a restraints file that should automatically link. I generated the file with eLBOW and then edited that atom names to be the standard main chain names. If you edit the PDB file to reflect the atoms it should use the standard peptide links. For the record, I changed N1 -> N CA1 -> CA C3 -> C O3 -> O 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 On Tue, Jun 2, 2015 at 8:15 PM, Kevin Jude <kjude(a)stanford.edu> wrote: > I just went through this with a blue FP. Carsten is correct about how to > define the peptide bonds, but an easier way is to use JLigand. The > tutorial at > http://www.ysbl.york.ac.uk/mxstat/JLigand/tutorial_link.html#link is > helpful. You will have to define the i-1 and i+1 links in separate .cif > files if you use JLigand. > > HTH > kmj > > On Tue, Jun 2, 2015 at 4:40 PM, Schubert, Carsten [JRDUS] < > CSCHUBER(a)its.jnj.com> wrote: > >> Hi Nat, >> >> >> >> bonds in COOT do not mean much, as they do not translate into bonded >> interactions in the refinement programs. Phenix for instance tries to >> figure out the bonding by itself through some distance based heuristics. >> However in your case it looks as if the CRO residue may not be defined as a >> polymer, i.e. part of a protein chain in the monomer library you are using. >> In Windows the monomer library is located in >> C:\WinCoot\share\coot\lib\data\monomers. Look at the difference in the >> headers for CYS.cif and CRO.cif or PTR.cif (phosphotyrosine). The >> aminoacids or modified aminoacids considered part of the peptide chain have >> all ‘peptide’ in the header, CRO does not. That is probably the reason why >> coot does not make any bonds. This would probably cause problems later on >> with Phenix as well. You could pull out the CRO.cif into your directory, >> modify it to make it a peptide and read it into coot and phenix during >> refinement. I would also run it through REEL to make sure the definitions >> are kosher. >> >> >> >> HTH >> >> >> >> Carsten >> >> >> >> >> >> *From:* Natalia Ketaren [mailto:[email protected] >> <nketaren(a)mail.rockefeller.edu>] >> *Sent:* Tuesday, June 02, 2015 5:42 PM >> *To:* Schubert, Carsten [JRDUS] >> *Subject:* Re: Changing an amino acid to an unusual amino acid >> >> >> >> Hi Carsten, >> >> >> >> Th residue is a part of the correct chain. It just doesn’t make an bonds >> with the residues on either side of it. Is this common for unusual amino >> acids when adding to the main chain? >> >> >> >> Cheers, >> >> >> >> Nat >> >> _____________________________ >> >> Natalia E. Ketaren, PhD >> Postdoctoral Associate >> Rout Laboratory >> Box 213 >> The Rockefeller University >> 1230 York Avenue >> New York, NY 10065 >> >> Tel: (212) 327-8136 >> Fax: (212) 327-7193 >> Natalia.Ketaren(a)rockefeller.edu >> website: http://lab.rockefeller.edu/rout/ >> NCDIR: http://www.ncdir.org/ >> >> >> >> On Jun 2, 2015, at 5:26 PM, Schubert, Carsten [JRDUS] < >> CSCHUBER(a)its.jnj.com> wrote: >> >> >> >> Hi Natalia, >> >> >> >> if the missing/wrong chain IDs are really the problem you can change them >> in COOT under Calculate -> Change Chain IDs. The dialog is a bit tricky, >> since you probably have to use the correct residue range to change an >> individual residue into an existing chain. In your case I would write out >> the PDB file and use a text editor to change the chain ID and move the >> residue into its correct place in the file. >> >> >> >> HTH >> >> >> >> Carsten >> >> >> >> *From:* phenixbb-bounces(a)phenix-online.org [ >> mailto:[email protected] >> <phenixbb-bounces(a)phenix-online.org>] *On Behalf Of *Natalia Ketaren >> *Sent:* Tuesday, June 02, 2015 5:17 PM >> *To:* phenixbb(a)phenix-online.org >> *Subject:* [phenixbb] Changing an amino acid to an unusual amino acid >> >> >> >> Hello All, >> >> >> >> I’m working on a GFP structure and I’m trying to incorporate the CRO >> (chromophore) residue into the structure using coot. My process is to use >> Extension->Modelling—>Replace residues, where it’s suppose to replace a Tyr >> residue. I type the 3 letter code, CRO, the residue appears, I’m able to >> real space refine it, but it does not incorporate CRO into the desired >> chain. Would someone be able to help me figure out what I’m doing wrong? >> And possibly walk me through a solution? >> >> >> >> Cheers, >> >> >> >> Nat >> >> _____________________________ >> >> Natalia E. Ketaren, PhD >> Postdoctoral Associate >> Rout Laboratory >> Box 213 >> The Rockefeller University >> 1230 York Avenue >> New York, NY 10065 >> >> Tel: (212) 327-8136 >> Fax: (212) 327-7193 >> Natalia.Ketaren(a)rockefeller.edu >> website: http://lab.rockefeller.edu/rout/ >> NCDIR: http://www.ncdir.org/ >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org >

10 years, 1 month

[phenixbb] Meeting Announcement: Northwest Crystallography Workshop

by Dale Tronrud

(Pacific) Northwest Crystallography Workshop http://oregonstate.edu/conferences/event/nwcw2014/ June 20-22, 2014 Registration is now open for this year's edition of the Northwest Crystallography Workshop. It is being hosted at Oregon State University in Corvallis in the heart of the Willamette Valley surrounded by wine country, wildlife refuges, and with both the Cascade Mountains and the Pacific Ocean within easy driving distance. It can be easily accessed from either the Portland or Eugene airports. This biennial meeting has been held at various locations in the Pacific Northwest since 1981. It has always proven to be a great venue to meet other researchers in the region who are interested both in using macromolecular crystallography to solve structures and in developing and enhancing methods. The "workshop" part of the name will be taken seriously. We will have talks and posters with priority for speaking slots given to students and post-docs who focus on methodologies or interesting structure determination stories, and/or how structural observations provide insight into function and biology. There will be a reception on Friday evening. On Saturday there will be talks during the day and a banquet followed by a keynote address in the evening. Talks will continue on Sunday morning with the workshop wrapping-up at noon. A light lunch will be served on Saturday and a boxed lunch will be available on Sunday. Register today and get your abstracts submitted anytime between now and the April 30 abstract deadline. We've tried to keep registration costs low and early registration (through April 30) is $75 for students and $100 for others. Reasonably priced on-campus dormitory housing is available and must be arranged at the time of registration. Special rates at two local hotels have been arranged for those who want to book their own lodgings. We look forward to a great meeting and celebration of the International Year of Crystallography. Dale and Andy Dale E. Tronrud and P. Andrew Karplus Department of Biochemistry & Biophysics 2011 ALS Bldg Oregon State University Corvallis, OR 97331 USA

11 years, 4 months

[phenixbb] Algorithm developer postdoc opening at Berkeley National Lab

by Nicholas Sauter

Berkeley Lab's Molecular Biophysics and Integrated Bioimaging Division <http://biosciences.lbl.gov/divisions/mbib/> is looking for a Computational Biologist Postdoctoral Fellow to work in the Sauter group. We are seeking an algorithm developer for the increasingly complex analysis of large diffraction datasets in structural biology. Current projects utilize XFEL crystallography and spectroscopy to investigate the photosynthetic mechanism of water splitting and to probe other metalloenzyme reactions. We also wish to test whether diffuse scattering can reveal correlated atomic motions in crystals. Many problems remain to be solved, including the details of how to optimally merge datasets from thousands of crystals. Our software development projects (including packages such as DIALS <http://dials.lbl.gov> and cctbx.xfel <http://cci.lbl.gov/xfel>) have been highlighted in several high-impact publications listed HERE <http://biosciences.lbl.gov/profiles/nicholas-sauter>. Candidates should have expertise in one or more computational techniques including, but not limited to, ray tracing to test underlying physical models of the diffraction, Bayesian approaches for refining model parameters, macromolecular modeling and refinement, neural networks for interpreting image features, as well as signal processing and denoising methods. Extensive data analysis experience in crystallography or from more general bioimaging backgrounds are welcome. We particularly encourage strong mathematical intuition and a track record of bringing new ideas and tools to fruition, as evidenced through written publication and clear presentation. Candidates should send an expression of interest, CV, and list of three references to *Nick Sauter, nksauter(a)lbl.gov <nksauter(a)lbl.gov>.* Further details are posted at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=82354. Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720

9 years, 2 months

Re: [phenixbb] smaller the cell parameter of EM map

by dancingdream＠163.com

Perfect! This problem bothering me for so long was finally solved! Thank you very much for your help! -- Wei Ding P.O.Box 603 The Institute of Physics,Chinese Academy of Sciences Beijing,China 100190 Tel: +86-10-82649083 E-mail: dingwei(a)iphy.ac.cn 在 2018-12-30 00:43:01，"Pavel Afonine" <pafonine(a)lbl.gov> 写道： Hi, have a look at the documentation: https://www.phenix-online.org/documentation/reference/map_box.html Reading through it I find this phenix.map_box map.mrc density_select=true should do it. Let us know if it doesn't. Pavel On 12/29/18 07:46, dancingdream(a)163.com wrote: Thanks for the quick replay! But my case is that no homology model for the target protein and it should be built directly from the em map. What should I do in this case ? -- Wei Ding P.O.Box 603 The Institute of Physics,Chinese Academy of Sciences Beijing,China 100190 Tel: +86-10-82649083 E-mail: dingwei(a)iphy.ac.cn At 2018-12-29 15:30:51, "Pavel Afonine" <pafonine(a)lbl.gov> wrote: Hi Wei, cutting out a box with model and map around it may be a solution for your case. A tool for this is phenix.map_box or its GUI equivalent. Pavel P.S.: phenix.real_space_refine does this internally so 'irrelevant' box size never affects runtime of refinement. On 12/28/18 23:14, dancingdream(a)163.com wrote: Dear all, The cell parameter of the EM map is always too large, which will make the model building program running very slow. But in factor, the structure is a smal part of cell. So can I smaller the cell parameter when I use phenix.map_to_structure_factors to convert the EM map to mtz file. Thank a lot! Wei _______________________________________________ phenixbb mailing list [email protected]://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org

6 years, 6 months

Re: [cctbxbb] flex index

by Ralf Grosse-Kunstleve

Hi Mona, Try this: from scitbx.array_family import flex a=flex.double([1,4,5,7,5,6,6,1]) a.set_selected(a > 5, 5) print list(a) Or in smaller steps: bool_selection = a > 5 assert bool_selection.size() == a.size() print list(bool_selection) a.set_selected(bool_selection, 5) print list(a) You can also call a.set_selected(bool_selection, b) where b is an array with as many elements as you have True in the bool_selection. This kind of working with selections is very typical within cctbx/phenix. If you look through our sources you'll find a lot of examples; in passing, we have two types of selections, bool selections as above, and integer selections. The latter are useful for permutations, e.g. to sort array elements, or if you know you select only a small number of elements from a large array. Let me know if you have more questions about selections and I'll be happy to explain. (I guess one day I should write a "Working with selections" tutorial.) Ralf On Tue, Oct 18, 2011 at 2:54 AM, Monarin Uervirojnangkoorn < monarin(a)biochem.uni-luebeck.de> wrote: > Hi, > > I'm using flex and 'd like to get an access to elements fall beyond/ below > certain value. eg. > a=[1,4,5,7,5,6,6,1] > anything beyond 5 should be set to 5. (in matlab then a(a>5)=5;) > if you could tell me how to do this quickly for flex, that would be great. > for now i use loop and that is... pretty slow. > > many thanks. > mona > > > > ^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^-^ > Institute of Biochemistry, > Institut für Neuro- und Bioinformatik, > Graduate School for Computing in Medicine and Life Sciences > University of Lübeck, > Ratzeburger Allee 160 > Lübeck 23538 > Germany > Tel: +49451-5004072 > Fax: +49451-5004068 > > > > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > >

13 years, 8 months

[cctbxbb] Algorithm developer postdoc opening at Berkeley National Lab

by Nicholas Sauter

Berkeley Lab's Molecular Biophysics and Integrated Bioimaging Division <http://biosciences.lbl.gov/divisions/mbib/> is looking for a Computational Biologist Postdoctoral Fellow to work in the Sauter group. We are seeking an algorithm developer for the increasingly complex analysis of large diffraction datasets in structural biology. Current projects utilize XFEL crystallography and spectroscopy to investigate the photosynthetic mechanism of water splitting and to probe other metalloenzyme reactions. We also wish to test whether diffuse scattering can reveal correlated atomic motions in crystals. Many problems remain to be solved, including the details of how to optimally merge datasets from thousands of crystals. Our software development projects (including packages such as DIALS <http://dials.lbl.gov> and cctbx.xfel <http://cci.lbl.gov/xfel>) have been highlighted in several high-impact publications listed HERE <http://biosciences.lbl.gov/profiles/nicholas-sauter>. Candidates should have expertise in one or more computational techniques including, but not limited to, ray tracing to test underlying physical models of the diffraction, Bayesian approaches for refining model parameters, macromolecular modeling and refinement, neural networks for interpreting image features, as well as signal processing and denoising methods. Extensive data analysis experience in crystallography or from more general bioimaging backgrounds are welcome. We particularly encourage strong mathematical intuition and a track record of bringing new ideas and tools to fruition, as evidenced through written publication and clear presentation. Candidates should send an expression of interest, CV, and list of three references to *Nick Sauter, nksauter(a)lbl.gov <nksauter(a)lbl.gov>.* Further details are posted at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=82354. Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720

9 years, 2 months

Re: [phenixbb] anomalous difference map

by Jason

On Sat, Mar 26, 2011 at 11:57 AM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > On Sat, Mar 26, 2011 at 9:45 AM, Jason <phenix.upitt(a)gmail.com> wrote: > > I was hoping to identify the ligand binding position by resolving the > > anomalous map first. Shouldn't this be the procedure to locate ligand? > > It depends on the ligand, I guess. If it's large enough and actually > bound, it should be detectable in the Fo-Fc map - this would be a good > sanity check to make sure that the anomalous map generation is working > properly. > Unfortunately my ligand is fairly small, about 12 atoms.The Fo-Fc map won't be that helpful. > > I know CCP4 can also generate anomalous difference map. But I myself have > > never done it (I googled online and found it not that straight forward). > Can > > anybody go through it for me please, or there are other handy programs > that > > can make anomalous difference map? > > You don't need to use CCP4 to make the map, just to process the data - > i.e. use MOSFLM/SCALA (xia2 will automate this), or you could also try > HKL2000, then use that as input for Phenix. But I doubt this is going > to give you a different answer. > XDS is the only program that is able to process my data (small oscillation angle and huge data file). On the other hand I am pretty sure xds is doing what it's supposed to do. I was more thinking of another program to generate anomalous map. Since it's phenixbb, probably it's not the right place :) > > Also: run Xtriage and look at the plot of anomalous signal vs. resolution. > > -Nat > ====================== Jason Structural Biology Department University of Pittsburgh ======================

14 years, 3 months

Search results for query "look through"