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Re: [phenixbb] Fo-Fo difference map for non-isomorphous datasets
by Jordan Luke Pederick 12 Mar '19

12 Mar '19

Also, I am interested if anyone knows of any publications that have included a real-space difference map? Cheers, Jordan ________________________________ From: Jordan Luke Pederick Sent: Monday, 11 March 2019 1:25:57 PM To: Eric Montemayor; Pavel Afonine; Philip Kiser; Tim Gruene; phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Fo-Fo difference map for non-isomorphous datasets Thank you all for the prompt responses and suggestions. My metal ion of interest is Cesium in this case, so I guess I am more interested in using this approach for visualization rather than peak identification - the strong density of Cs is fairly obvious I have attached a few images of the superimposed (Fo, Phi) maps and resulting difference map using either Superpose maps in phenix or transform_map in coot following Tim's suggestions. I also tried using maprot (CCP4) to apply the rotation/translation operator from the LSQ superpose but the resulting map was not superposed correctly (not sure why). Both results seem kind of reasonable - I have shown one of the difference peaks for what is likely to be a bound Cs. For both approaches the peak was very obvious at a 3 sigma level, and could still be observed to around 10 sigma in both cases. I am still unsure about differences in scaling, so although strong positive peaks can be identified, I wouldn't be confident using the map to interpret smaller differences. In response to Eric - I checked the anomalous signal, which was fairly weak. The resulting anomalous difference map did show positive peaks up to a level of ~10 sigma that matched those observed in the above real-space difference maps, with a 3 sigma level corresponding to 0.0137 e/A^3. The CCanom was also low (1-5% between shells), so I was thinking that another approach might be more suitable for this data? Cheers, Jordan ________________________________ From: Eric Montemayor <montemayor.eric(a)gmail.com> Sent: Sunday, 10 March 2019 4:50:21 AM To: Jordan Luke Pederick Subject: Re: [phenixbb] Fo-Fo difference map for non-isomorphous datasets Why not just look for peaks in the anomalous difference Fourier for just the derivative dataset? If there’s even a weak anomalous signal, you won’t need to mess with non-isomorphism between multiple datasets.... the information you need is already contained alone in the derivative dataset. What is the metal? The above approach won’t work for something like magnesium, but should work for almost any transition metal. Eric On Sat, Mar 9, 2019 at 3:23 AM Jordan Luke Pederick <jordan.pederick(a)adelaide.edu.au<mailto:[email protected]>> wrote: Hi, I am trying to generate a Fo-Fo difference map for two data sets of the same protein at ~2.3 angstrom resolution. One dataset is native and the other was soaked with a metal ion, so the purpose of the map is for identifying and visualizing peaks that may correspond to a bound metal ion. These datasets differ by 6 angstroms (~10%) along the A edge - an isomorphous difference map generated in Phenix GUI wasn't useful As an alternative I was planning to make a real-space Fo-Fo difference map making use of Superpose Maps in Phenix Gui as follows: Superpose maps would be used to superimpose (Fobs.metal, PHI.metal) and (Fobs.native, PHI.native) The superimposed maps will be opened in Coot and a difference map generated using "Extensions -> Maps -> Make a difference map" There were two things I was unsure about: Does this seem like a reasonable alternative? Is scaling of the two datasets required before generating the difference map? Cheers, Jordan _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]>

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phenix.elbow error
by Eugene Osipov 10 Mar '19

10 Mar '19

Dear phenix developers, I have found that QM calculations in phenix.elbow fail due to an error: *bad fp number.* I've found the source of the error in phenix-1.14-3260/modules/elbow/elbow/quantum/run_utils.py at line 11: easy_run.call('./%s.csh >& /dev/null' % project) should be : easy_run.call('./%s.csh 2>&1 /dev/null' % project) Also jaguar template (phenix-1.14-3260/modules/elbow/Jaguar.csh) is a bit outdated. For $SCHRODINGER/jaguar paramether -PROC was replaced by -PARALLEL also, it seems that programs seeks for wrong input file. So I suggest that: $SCHRODINGER/jaguar run -PROCS %d -WAIT $PROJECT should look like: $SCHRODINGER/jaguar run -PARALLEL %d -WAIT $PROJECT.in Can you please fix this issues in next releases? -- Evgenii Osipov Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU Leuven O&N2

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Fo-Fo difference map for non-isomorphous datasets
by Jordan Luke Pederick 09 Mar '19

09 Mar '19

Hi, I am trying to generate a Fo-Fo difference map for two data sets of the same protein at ~2.3 angstrom resolution. One dataset is native and the other was soaked with a metal ion, so the purpose of the map is for identifying and visualizing peaks that may correspond to a bound metal ion. These datasets differ by 6 angstroms (~10%) along the A edge - an isomorphous difference map generated in Phenix GUI wasn't useful As an alternative I was planning to make a real-space Fo-Fo difference map making use of Superpose Maps in Phenix Gui as follows: Superpose maps would be used to superimpose (Fobs.metal, PHI.metal) and (Fobs.native, PHI.native) The superimposed maps will be opened in Coot and a difference map generated using "Extensions -> Maps -> Make a difference map" There were two things I was unsure about: Does this seem like a reasonable alternative? Is scaling of the two datasets required before generating the difference map? Cheers, Jordan

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Units in intensity?
by Murpholino Peligro 09 Mar '19

09 Mar '19

If I do `phenix.xtriage XDS_ASCII.HKL` I get a log file. In the "Statistics for data merging" of this log file I have: Resolution: 26.02 - 1.40 Observations: 44675 Unique reflections: 16306 Redundancy: 2.7 Completeness: 70.37% Mean intensity: 1656.8 Mean I/sigma(I): 19.8 SigI < 0 (rejected): 644 observations R-merge: 0.027 R-meas: 0.032 R-pim: 0.017 My question is... what units does Mean intensity has? Thanks Ps I am not sure if this has to do with the detector used which was a CCD (type) ADSC QUANTUM 210 (model).

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difference in Wilson B calculated in Xtriange or Polygon
by Eze Chivi 08 Mar '19

08 Mar '19

Hi, The value of Wilson B calculated in Phenix differs for the same data when I use Polygon or Xtriange, why? In Xtriange-->Absolute scale and Wilson analysis: ML estimate of overall B value: 48.88 A**2 In Polygon: 52.05 Thank you Ezequiel

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contour values for Polder and FEM
by V F 07 Mar '19

07 Mar '19

Hi all, What is the recommended values for contouring for Polder and FEM? In pymol, I have a isomesh polder_COA_mesh, polder_207_1, 3, select_COA, carve=2 isomesh FEM_COA, fem_coa_190, 1, select_COA, carve=2 Are these sensible values? Many thanks, Vero PS: Both identify ligand very well!

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AUC2019 – registrations are open.
by Renwick Dobson 06 Mar '19

06 Mar '19

Dear Structural Biology community, AUC2019<https://auc2019.uleth.ca/>, the 24th AUC Workshop and Symposium, will be held at the University of Canterbury, Christchurch (New Zealand) from 24-29 August 2019. The format of the event is a 2-3 day workshop<https://auc2019.uleth.ca/workshops.php> offering parallel, hands-on training in experimental design and the latest AUC data analysis software from the world experts in this area followed by a 2 day research symposium on AUC and complementary approaches: methodological development, combination with orthogonal techniques (SAXS, SANS, SPR, MST, SEC-MALLS etc), application in biosciences and material sciences. Registrations are now open and details can be found at this website: https://auc2019.uleth.ca/ As the scientific program<https://auc2019.uleth.ca/symposium.php> for AUC2019 emerges, events will be uploaded to the website. We strongly encourage you to submit abstracts for talks and posters<https://auc2019.uleth.ca/abstracts.php>. The meeting is also timed such that delegates can also attend the Queenstown Molecular Biology Conference<https://www.queenstownresearchweek.org/> (which is in Queenstown), although note that this is a separate conference. Lastly, The European Biophysics Journal has kindly agreed to run a special issue to celebrate the research presented at AUC2019. Therefore, we invite those who wish to extend their talks to a journal publication to consider contributing original research articles to this issue. Please indicate your interest for inclusion in this volume below. Deadline for registration of a contribution is August 30 2019. We look forward to welcoming you to Christchurch, New Zealand next Spring(-ish)! Ren Dobson, Chair AUC2019 On behalf of the AUC2019 Scientific Organising Committee ---- Prof. Ren Dobson Co-Director, Biomolecular Interaction Centre (BIC) http://www.bic.canterbury.ac.nz/ School of Biological Sciences | Te Kura Pūtaiao Koiora University of Canterbury | Te Whare Wānanga o Waitaha Private Bag 4800 Christchurch | Ōtautahi New Zealand | Aotearoa E: renwick.dobson(a)canterbury.ac.nz<mailto:[email protected]> T: ++64 (03) 369-5145 x 95145 F: ++64 (03) 364-2590 W: http://dobsonlab.org/

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Postdoctoral position in structural biology of influenza virus transcription Cusack group, EMBL Grenoble
by Stephen Cusack 05 Mar '19

05 Mar '19

Postdoctoral position in structural biology of influenza virus transcription Cusack group, EMBL Grenoble We are looking for a highly motivated and ambitious individual to progress our understanding of the mechanism of transcription by influenza virus RNA-dependent RNA polymerase. The work is in the frame of the ANR-funded FluTranscript project that brings together the complementary expertise of the groups of Stephen Cusack (EMBL Grenoble, project coordinator) and Nadia Naffakh (Institut Pasteur) in structural biology and molecular virology, respectively. The project follows on from a recent joint publication (Structural basis of an essential interaction between influenza polymerase and Pol II CTD. Lukarska et al, Nature 2017) and aims to reconstitute and determine the structure of functional transcription complexes. A secondary goal is to use the acquired structural information to develop new approaches to anti-influenza drug development. The Cusack group uses X-ray crystallography and cryo electron-microscopy to study the structural biology of protein-RNA complexes involved in RNA virus replication, innate immunity and cellular RNA metabolism. Group website: https://www.embl.fr/research/unit/cusack/index.html The successful candidate should have a PhD in Molecular Biology or related field and a strong background and interest in biochemistry and structural biology. We are looking for a creative and ambitious person with good communication skills and keen to work on a challenging project. Experience in insect cell expression systems, reconstitution of protein-RNA complexes, X-ray crystallography or cryo-electron microscopy would be particularly beneficial. EMBL is one of the world’s leading research organizations in the life sciences. The Headquarters Laboratory is located in Heidelberg, with additional sites in Barcelona, Grenoble, Hamburg, Hinxton, and Rome. EMBL Grenoble has excellent access to state-of-the-art structural biology technologies with the in house EM facility being equipped with a T12 microscope and 200kV Glacios/Falcon III . Additionally, we have access to the Titan Krios at the adjacent ESRF as well as those in EMBL Heidelberg. Other facilities on the Grenoble Campus include the ESRF synchrotron X-ray beamlines, neutron scattering at the ILL, high-field NMR at the IBS as well as high-throughput crystallization platform, mammalian and insect cell facilities, biophysical platform and confocal microscopy. You can find out more about this vacancy at: https://www.embl.fr/jobs/searchjobs/index.php?ref=GR00133 or by contacting Stephen Cusack: cusack(a)embl.fr Please apply online through www.embl.org/ Stephen Cusack -- ********************************************************************** Dr. Stephen Cusack, FRS Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL) Group leader in structural biology of protein-RNA complexes and viral proteins ********************************************************************** Email: cusack(a)embl.fr Website: http://www.embl.fr Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 Fax: (33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France **********************************************************************

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Are TLS parameters applied when TLS refinement is OFF?
by Mark Saper 05 Mar '19

05 Mar '19

I have a structure where at one stage TLS parameters were determined and then refined. It caused the R-free to increase so I stopped refining the TLS parameters. Are the TLS parameters still applied to the structure on subsequent refinement runs even when the TLS refinement is off? Is it appropriate to refine anisotropic B’s for a high resolution (1.35 Å) structure AND apply TLS parameters? Thanks, Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353 mobile: (734) 276-6505

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MAD merged dataset deposition
by Eugene Osipov 03 Mar '19

03 Mar '19

Hello, everyone, I have solved the structure of heme containing protein using anomalous signal from Fe atom (~1.739 anstroms) and further refined it using native dataset (0.9 angstroms). Structure was solved in AutoSol. The question is "What is the best way to deposit mtz with both datasets?" Should I merge and scale them simultaneously or can I deposit output file from AutoSol overall_best_refine_data.mtz, which contains F,FP, Rfree and HL coefficients? P.S.: please, respond in PM, I have only digest subscription on phenixBB. Thank you in advance! -- Evgenii Osipov Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU Leuven O&N2

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