May 2014 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

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how to refine everything except n residues in phenix.refine?
by Murpholino Peligro 22 Oct '14

22 Oct '14

Hi everybody! Everytime when I (within coot) do "real space refine" two arginines that have two alternate conformations ..(interacting by hydrogen bonds); and then phenix.refine everything, both conformers move away. Therefore, when I open my mtz and pdb files from phenix.refine in coot, I'll have green blobs where there should be guanidium groups. Can I tell phenix.refine not to move only those two residues? It should be something like the following lines in the eff file? sites { individual = None torsion_angles = None rigid_body = None remove_selection=resid 45 remove_selection=resid 68 } Thank you very much

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GUI program to calculate effective resolution of a data set
by Alexandre OURJOUMTSEV 19 Jun '14

19 Jun '14

Dear All, Recently, there was a ccp4bb conversation concerning the definition of a ‘real’ (effective) resolution of (incomplete) diffraction data sets. I am happy to announce that a corresponding GUI program EFRESOL is available now and you may download it from the Web site: http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/efresol/Efresol.html http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Sites.html The method is described in L.Urzhumtseva, B.P.Klaholz, A.Urzhumtsev (2013) Acta Cryst., D69, 1921-1934. We would like to thank Joel Bard, Tom Peat, Rajan Prabu and especially Boaz Shaanan for testing the original version of the program. With best wishes, Sacha Urzhumtsev

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molecular replacement keeping hetatms?
by Murpholino Peligro 27 May '14

27 May '14

Can I do molecular replacement with phenix/phaser, keeping all the waters from the first model from the first data set? >From here ( http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#WATER), I should change all the HOH labels to something like WWW. Then I guess that I should put HOH labels again in the solution model, for the following refinement in phenix.refine. Is that it?... Any suggestions? thanks again!

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(no subject)
by Fulvio Saccoccia 27 May '14

27 May '14

Dear phenix users and developers, in the past I usually used the fix_rotamers=true options to fix some residue issues. Now, this option is lacking (I currently use the dev-1702 version of phenix) but I was wondering if some other option does replace it. In addition, I would like to know better how real_space_refinement works; is there any tutorial or presentation about it? Thanks in advance -- Fulvio Saccoccia, PhD Dept. of Biochemical Sciences Sapienza University of Rome 00185, Rome (Italy) Phone: +39 06 4991 0556 https://www.researchgate.net/profile/Fulvio_Saccoccia/?ev=hdr_xprf

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Workshop announcement @ Inst Pasteur Montevideo - Uruguay : Modern Approaches in Drug Discovery for Neglected Infectious Diseases
by Alejandro Buschiazzo 23 May '14

23 May '14

Dear Colleagues: We are pleased to announce the Workshop: "Modern Approaches in Drug Discovery for Neglected Infectious Diseases" at the Institut Pasteur de Montevideo (Uruguay). *Dates:* November 3rd - 8th, 2014 *Venue**: *Institut Pasteur de Montevideo (Montevideo, Uruguay) *Invited speakers:* Wim Hol (University of Washington, Seattle, USA), Paul Michels (University of Edinburgh, Edinburgh, UK), Celerino Abad-Zapatero (University of Illinois at Chicago, Chicago, USA), Hugo Cerecetto (UdelaR), Marcelo Comini (IP Montevideo), Sergio Pantano (IP Montevideo), Alejandro Buschiazzo (IP Montevideo)* * *Aim:* The general aim of this International Workshop is to train students in state-of-the-art approaches for drug discovery and rational design, with special emphasis on target-based methods. The course will provide with a multidisciplinary view, with invited professors covering a diverse set of subjects : protein crystallography, in silico methods for molecular simulations, medicinal chemistry and biology of neglected infectious diseases.** For details of the activity please see the preliminary program. <http://www.pasteur.edu.uy/images/program_v.5-5-14.2.pdf> The course will be in English. This activity is supported by the /Center for Structural Biology of the MERCOSUR /(CeBEM <http://www.cebem.org.ar/>), jointly with the /United Nations University Biotechnology Programme for Latin America and the Caribbean/ (UNU - BIOLAC <http://unu.edu/about/unu-system/biolac>). * **Applicants:* Graduate students and young research scientists are encouraged to apply. 24 students will be selected among the applications. The Course will provide financial support for the students, covering registration fees, and for the case of those coming from abroad, all local expenses (lodging, per diem and local transportation). /* The application deadline is September 8th, 2014. The results will be announced by September 30th.*/ The application form, activity program, contact information and other details can be found at the web site of the course <http://www.pasteur.edu.uy/index.php/en/teaching/courses/54-ensenanza/cursos…> Please address further inquiries toSBDD_course(a)pasteur.edu.uy <mailto:[email protected]> Looking forward to welcoming you in Montevideo! -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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Three positions open at the MAX IV Laboratory
by Marjolein Thunnissen 23 May '14

23 May '14

The MAX IV facility, the largest and most ambitious Swedish investment in research infrastructure, will be the brightest source of x-rays worldwide and will replace the existing laboratory, which today consists of the storage rings MAX I, II and III. The new MAX IV facility will become operational in June 2016. To extend the suite of already funded beamlines, MAX IV Laboratory is planning the next set of beam lines. Therefore The MAX IV laboratory in Lund has opened two positions within the life-science division. We are looking for two beamline scientists, one for the biomedical imaging beamline MEDMAX and one for the microfocus beamline MicroMAX. For both these positions the scientist will be overseeing the development, construction and commissioning of the MedMAX, respectively MicroMAX beamline from its conceptual stage to full operation. Both beam lines are planned to be cutting edge beam lines, fully exploiting the excellent properties of the MAX IV 3GeV storage ring. In addition we are also looking for a software engineer to be engaged in the design of the MX software infrastructure at the beamline for protein crystallography which is under construction, BioMAX. More information on these positions can be found at https://www.maxlab.lu.se/positions and the links within this page, or from our Life-Sciences director Tomas Lundqvist . best regards Marjolein Thunnissen [cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC] Marjolein Thunnissen Science Coordinator MX MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se<http://www.maxlab.lu.se/>

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Integrated Structural Biology, PhD program at the IGBMC
by Alexandre OURJOUMTSEV 21 May '14

21 May '14

Dear all, kind reminder for PhD fellowship opportunities at the International PhD program of the IGBMC, notably for Integrated Structural Biology. Deadline for applications is 3rd of june 2014: http://phdprogramme.igbmc.fr/ Interested candidates are invited to visit the home pages of the teams of the Integrated Structural Biology department at http://www.igbmc.fr/research/department/3/ Please feel free to contact the group leaders for further information about the projects. Best regards, Bruno Klaholz Sacha Urzhumtsev

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any idea what is this? (unidentifiable blob in electron density map)
by Murpholino Peligro 21 May '14

21 May '14

1) 2FOFCWT PH2FOFCWT bue map (front1.png) (process: XDS->Aimless within CCP4i->MR with Phaser->Phenix.refine/coot->Phenix-refine-withwaters/coot) 2) FWT PHWT purple map (front2.png) (Output from Aimless and calculate Fs with refmac within coot with last pdb from 1st line) What do I have in the crystal? NaCl, Sodium acetate, water, lysozyme and some complexes (~ 400 daltons) that chelate Cu2+ Is there like a gallery of crazy-looking blobs that are explained with something ....real and possible? (that would be great help for the newb) Thanks in advance. links to screenshots right here: https://www.dropbox.com/s/rzjepvr8genolxi/front1.png https://www.dropbox.com/s/0iycf4lh5y726x4/front2.png https://www.dropbox.com/s/xx5kvgn91p763ei/faraway.png (1.0 rmsd for both maps above and 3.5 for the "red and green maps")

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phenix.rna_validate and the MolProbity web server report different bond angle violations
by Huw Jenkins 20 May '14

20 May '14

Hi, I’ve recently been using phenix.erraser to help correct RNA geometry errors and finding it very useful. However, it appears that the geometry validation statistics reported by phenix.rna_validate with respect to bond angle outliers are very different from those reported by the MolProbity web server. As an example - if I run phenix.rna_validate on 1u8d (as used in the documentation for phenix.erraser) the following outliers are reported: RNA Validation ----------------------------------------------- Pucker Outliers: #residue:delta_angle:is_delta_outlier:epsilon_angle:is_epsilon_outler G A 15 :74.054:no:103.458:yes U A 48 :119.081:yes:283.965:no U A 63 :90.366:yes:74.220:yes ----------------------------------------------- Bond Length Outliers: #residue:atom_1:atom_2:num_sigmas ----------------------------------------------- Angle Outliers: #residue:atom_1:atom_2:atom_3:num_sigmas C A 39 : C5': C4': C3':-5.294 U A 63 : O3': C3': C2':-4.402 ----------------------------------------------- Suite Outliers: #suiteID:suite:suiteness:triaged_angle G A 16 :!!:0.000:epsilon-1 U A 48 :!!:0.000:delta U A 49 :!!:0.000:delta-1 A A 64 :!!:0.000:epsilon-1 The MolProbity web server reports the same pucker and suite outliers but flags up many more angle violations: A 39 C worst is C5'-C4'-C3': 10.588 σ A 63 U worst is O3'-C3'-C2': 8.803 σ A 54 C worst is C5'-C4'-C3': 7.883 σ A 49 U worst is C2'-C1'-N1: 5.416 σ A 62 G worst is C2'-C1'-N9: 4.946 σ A 15 G worst is O3'-C3'-C2': 4.825 σ A 22 U worst is C5'-C4'-C3': 4.785 σ A 64 A worst is C4'-C3'-O3': 4.648 σ A 65 A worst is C2'-C1'-N9: 4.582 σ A 44 A worst is C4'-C3'-C2': 4.395 σ As the number of sigmas for the angle violations are different between phenix.rna_validate and MolProbity I guess they’re using different target distributions (not just reporting at a different sigma cut-off) but I’ve no idea which is more valid. Hopefully there is a simple explanation! Thanks, Huw

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