March 2012 - phenixbb - phenix-online.org

Hydrogens
by Christopher Wanty 21 Mar '12

21 Mar '12

Hi all, I've been refining with riding hydrogens, and from what I've read hydrogen contribution should be included in Fo calculation automatically for maps. What I'm seeing after refinement is a lot of little bits of green in the difference density that look like they could be explained by hydrogens. I'm working at 1.4A, attached image gives an example and shows contours at 3 sigma for difference map. Is there a setting/parameter I need to adjust to get this to work properly? Kind Regards, Chris ------------------------------------------------------- Dr. Christopher Wanty christopher.wanty(a)uwa.edu.au Research Associate Biomolecular, Biomedical and Chemical Sciences, Building M310 University of Western Australia 35 Stirling Highway Crawley 6009 Western Australia Australia

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building a peptide-like polymer with phenix.elbow
by Geoffrey Feld 21 Mar '12

21 Mar '12

Greetings, I have a co-crystal structure of a protein bound to an interesting polymer -- poly-D-g-glutamic acid (poly glutamic acid with D chirality and gamma linked, rather than alpha linked). In the structure, I have density corresponding to different links, from 1 to 6 (so far). I'd like to build a ligand that has "residues" much like a polypeptide polymer so that I can refine each residue individually (hopefully in COOT). Up till now, I've been using SMILES to generate the different length polymers so I have pdbs and cif files, and then (painstakingly) modelling them into COOT, building restraints for refinement, etc. More recently, I used maestro to build a dimer that at least has the right atom labels you'd expect for a protein. However, I can't use phenix now to generate cif files because it is confused by the GLU. Is there a way to use phenix.elbow to make a multi-residue polymer? I'm also doing some monte carlo minimizations in macromodel to generate models of the various low energy states and would like to use them as building blocks, so an easy order-of-operations would be to generate the files in macromodel and feed them in via pdbs to phenix.elbow to generate cif restraints. Any help on this would be greatly appreciated. Cheers, Geoff -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

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a small trick for SDS-Gel storage
by Kevin Jin 21 Mar '12

21 Mar '12

Dear All, Maybe most of you already knew. I just put my understanding of SDS page gel storage here, if you want to make gel yourself and safe some money. http://www.jinkai.org/SDS_page.html If I am wrong, please let me know. Sharing knowledge each other is always joyful. -- Kevin Jin Protein crystallographer and Biopolymer chemist Personal Website: http://www.jinkai.org/

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A possible conjugative relaxase with novel fold for DNA cleavage?
by Kevin Jin 20 Mar '12

20 Mar '12

Dear All, The protein structure of Jann_2411 (PDB 3H0N) from Jannaschia sp. strain CCS1 carries a novel fold for unknown function. Zn-finger is indentified in the C-terminus. However, the N-terminus with a metal binding site presents a novel fold. As the person who solved and characterized this protein, I would like to put some further observation here for your consideration. My analysis is available here: http://www.jinkai.org/Novel_fold_3H0N.html Best regards, Kevin -- Kevin Jin Protein crystallographer and Biopolymer chemist Personal Website: http://www.jinkai.org/

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NCS operators
by Melania Strycharska 20 Mar '12

20 Mar '12

Dear all, I have a bit of a problem applying NCS to my fairly low resolution structure. If I try to look for NCS symmetry automatically - phenix doesn't find any. If I specify sections that I want to be related by NCS, the script usually crashes. I have a dimer in the asymmetric unit, however it appears that one domain is related by 3-fold symmetry while the other is related by 6 fold symmetry. I can "cheat" phenix and generate operators for each of the domains by feeding a stripped pdb file (one that contains only a dimer of one domain or the other) to phenix.simple_ncs_from_pdb and then it easily identifies the ncs operators... unfortunately the simple_ncs_from_pdb.ncs file generated that is meant to be fed into phenix.refine contains only the chain selections, not the actual operators. Is there a way to specify different NCS operators (rotational matrix and translational vector) for specific chain selections in the .eff file or under GUI? or if there isn't, how can I still take advantage of my NCS symmetry? Also, is there any obvious reason why NCS operators that I generated with Phenix do not match the operators that I found using CCP4 Lsqkab? (yes I already accounted for chain A moving onto B or chain B moving onto A) Can I choose to apply NCS symmetry to just my backbone? How would I specify that? thanks so much! Melania

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GUI parameter files
by Leonid Sazanov 19 Mar '12

19 Mar '12

Hi, I have a following problem in dev-874 version: If I restore a previous job in refine GUI, to run it with modified settings, and include a new parameter file .eff with definitinon of secondary structure restrains, these new restrains are combined with previously used restrains. How do i get rid of previous restrains? Older file is not visible in inputs, but its settings are still used. And in general, how can one be sure which parameters are used at the start of each refine run? If older settings loaded from .eff or .param file are not visible, the only way is to look through new .eff file, which takes a lot of time. Has this been solved in latest builds perhaps? Thank you, Leo -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Refinement using data with pseudo translational symmetry
by Bret Wallace 18 Mar '12

18 Mar '12

To all, First I apologize for the long email, but I wont to make sure that I give enough information to describe the problem. I have been working on a structure of two proteins in complex with each other (one forms a homodimer, with each monomer bound to 1 monomer of the other protein), using data, that according to phenix.xtriage contains pseudo translational symmetry (output pasted below). I have done a lot of searching of both the phenixBB and ccp4BB regarding solutions to this problem, but unfortunately most responses seem to be directed at resolving issues with MR. I have successfully performed MR using both phenix phaser, ccp4 phaser (the most updated version), as well as molrep. The issue arises upon structure refinement, where my Rwork and Rfree are essentially stuck at 28 and 33, respectively. I have built the entire structure, including ligands, except for any solvent molecules. Here are the details for the data/structure: SG: P212121 Cell: 72 124 175 90 90 90 Res: 50-2.8 Patterson analyses ------------------ Largest Patterson peak with length larger than 15 Angstrom Frac. coord. : 0.155 0.000 0.500 Distance to origin : 87.222 Height (origin=100) : 34.517 p_value(height) : 6.739e-04 The reported p_value has the following meaning: The probability that a peak of the specified height or larger is found in a Patterson function of a macro molecule that does not have any translational pseudo symmetry is equal to 6.739e-04. p_values smaller than 0.05 might indicate weak translational pseudo symmetry, or the self vector of a large anomalous scatterer such as Hg, whereas values smaller than 1e-3 are a very strong indication for the presence of translational pseudo symmetry. Xtriage notes that the if the PTS is crystallographic, that C2221 is a possible SG (x+1/6, y, z+1/2). However, neither XDS or HKL picks orthorhombic C, and the indexing/integrating doesn't work if I force it. I should also not there is no twinning detected by either xtriage or twinning servers. I have done a number of things to try to resolve this: -rescaling in lower symmetry (P21 and P1) -rescaling in the PG P222 and letting the MR program decide the proper space group -shifting origin and re-refining -a number of different refinement protocols (TLS, optimized weights/adp, simulated annealing, several cycles of rigid body, etc.) I have used HKL2000 and XDS to index/integrate/scale the data, both yield the same results, with slightly different completeness and Rmerge values, but refining with either gives similar R factor values. Does any know of any other possible things I should try to refine this data? I am happy to provide additional information upon request. Thanks in advance for any help! Bret

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selectively remove bond length restraints on atoms
by Maxime Cuypers 15 Mar '12

15 Mar '12

hello, What is the best way to selectively remove bond length restraints on some selected atoms for phenix.refine? i found the commands for a .param file: refinement { geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } } but no bond length command in the manual online. http://www.phenix-online.org/version_docs/dev-283/refinement.htm otherwise there is the commands refinement { geometry_restraints.edit { bond { action= *delete change atom_selection_1= (selection1 here) atom_selection_2= (selection2 here) distance_ideal= None } } } is it a good way to deal with the problem ? thanks in advance for your help. Maxime

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crystal packing pattern
by bsubedi＠btk.fi 15 Mar '12

15 Mar '12

Hi All, Could someone help me with a program/tool to see the pattern of protein packing in the crystal. I would like to make comparative study between regions of the protein in two different chains and if crystal packing has some effect on conformational alteration. Kind regards, World

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Reminder: BCA/CCP4 Summer School 2012
by Airlie McCoy 15 Mar '12

15 Mar '12

This is a reminder that applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Tuesday 28th August to Sunday 2nd September 2012. Applications close 1st May 2012. The course is suitable for PhD students in macromolecular crystallography who started in or before October 2011, and postdocs new to macromolecular crystallography. Please note that references from supervisors are also due by 1st May 2012, so don't leave your application until the last minute! For more information see: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School-2012.html Application form: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School-2012/Application-Pag…

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Transfer to new computer
by Colin Levy 15 Mar '12

15 Mar '12

Hi, Is it possible to transfer Phenix along with it's archive to a new computer? I have a fresh install of Phenix on the new machine and a copy of all the original files and folders from the old machine but cant figure how to point Phenix to the correct place. Thanks Colin

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March 15, 2012 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 Mar '12

14 Mar '12

Dear Users, The deadline for May/June 2012 Collaborative Crystallography proposals will be *Mar 15, 2012. * ------------------------------------------------------------------------ Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ------------------------------------------------------------ ----------------------------- How To Apply: To learn more, go to: http://www.als.lbl.gov/als/quickguide/becomealsuser.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for May/June 2012 allocation period, proposals must be submitted by *March 15, 2012.* The deadline for CC proposals for the time period July/August 2012 will be May 15, 2012. Regards, Banumathi Sankaran

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David Sayre
by Paul Adams 12 Mar '12

12 Mar '12

On behalf of the Phenix development team: We regret deeply the passing of David Sayre on Feb. 23, 2012. David Sayre made profound contributions to crystallography and scientific computing that continue to have a major impact decades later. An obituary summarizing his many achievements was posted by Physics Today (http://www.physicstoday.org/1.2732466). In crystallography, Sayre’s fundamental insight into the implications of the atomic nature of crystal structures and the relationships between crystallographic structure factors allowed him to develop in 1952 the brilliantly simple Sayre equation relating each structure factor to all other structure factors. The Sayre equation has had a well-known yet greatly under-appreciated significance in small-molecule crystallography, both in its original form and in the equivalent probabilistic forms implemented later as part of direct methods. These methods have profoundly affected macromolecular crystallography in the last decade because of their astounding power for determination of heavy-atom substructures. The use of direct methods has made possible solution of the positions of as many as 160 selenium atoms in large macromolecular structures. To appreciate the feat that this represents, it is useful to consider that many macromolecular crystallographers were initially hesitant to use the seleno-methionine approach at all for structures that had more than about 10 selenium atoms for fear that the substructure could not be solved. Sayre’s recent work on phasing X-ray diffraction data from single large objects such as a yeast cell and single small objects such as a single protein molecule was groundbreaking in a different way. This work is revolutionary because of its boldness, and because of the elegantly simple approach to phase determination that Sayre developed. Once again Sayre took a fundamental real-space feature of the diffraction image and used it to obtain phase relationships. In this case the diffraction forms a continuous pattern from a single object, and the feature is the lack of contrast outside of the object. While the idea of using a mask of the object (the “support”) to define phases has been used for some time in many contexts, it was far from obvious that this could be done with a single cell or with a single protein molecule. Sayre and his colleagues systematically showed theoretically and then experimentally that each step in this process can be carried out and that the required signal can be extracted to obtain an X-ray image of microdots and later even a yeast cell. Others have followed up his ideas for phasing data from a single protein molecule. This work was of fundamental and transforming importance because few would have believed that the ideas were remotely feasible, and now they have a sound theoretical basis and experimental demonstrations, allowing anyone to think of new and powerful ways to use these approaches. The breadth of Sayre's intellectual spectrum reached far beyond crystallography. He was also a member of the IBM team that developed the original Fortran compiler, the first high-level programming tool (see http://www.ibm.com/ibm100/us/en/icons/fortran/team/ for more details). Currently, 55 years after the first commercial release of Fortran, this language is still in wide use. The history of crystallographic computing, and scientific computing in general, cannot be separated from the success of Fortran, made possible by the amazing IBM team that included Sayre. In spite of his great accomplishments, David Sayre was modest and approachable in person, and he was generous in sharing credit with his colleagues. He will be greatly missed. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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phenix.elbow problem
by Simon Kolstoe 12 Mar '12

12 Mar '12

Hi there, Who's the best person to talk to when phenix.elbow is not assigning correct geometry to a molecule? Thanks, Simon --------------------------------------------------------------- Dr Simon Kolstoe Laboratory for Protein Crystallography Wolfson Drug Discovery Unit University College London Rowland Hill Street, London NW3 2PF Tel: 020 7433 2765 http://www.ucl.ac.uk/~rmhasek ---------------------------------------------------------------

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error after adp refinement
by Christian Roth 10 Mar '12

10 Mar '12

Dear Phenix Team, I started a refinement with anisotropic adp and weight optimization and directly after the optimization step an error appeared which never appeared befor for me. The previous steps of mask optimization and xyz refinement worked well. Best Regards Christian AssertionError : Traceback: File "/userdata-2/christian/phenix- dev-979/cctbx_project/libtbx/thread_utils.py", line 229, in run return_value = self._target(self._args, self._kwargs, self._c) File "/userdata-2/christian/phenix- dev-979/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__ result = self.target() File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/runtime.py", line 68, in __call__ call_back_handler=callback) File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/command_line.py", line 97, in run call_back_handler=call_back_handler) File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/driver.py", line 1494, in run ncs_manager = self.ncs_manager) File "/userdata-2/christian/phenix- dev-979/phenix/phenix/refinement/strategies.py", line 1046, in refinement_machine h_params = h_params) File "/userdata-2/christian/phenix- dev-979/cctbx_project/mmtbx/refinement/adp_refinement.py", line 212, in __init__ nproc = nproc) File "/userdata-2/christian/phenix- dev-979/cctbx_project/mmtbx/refinement/adp_refinement.py", line 389, in __init__ compute_gradients=False).target_work()) Platform info: __FILE__ = /net/longnose/scratch2/phenix/phenix- dev-979/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Feb 7 2012 __TIME__ = 02:05:24 __i386__ __linux __GNUC__ = 3 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 2 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 BOOST_LIB_VERSION = 1_48 PY_VERSION = 2.7.2 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 4 sizeof(std::size_t) = 4 sizeof(void*) = 4 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 12 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 gnu libc version: 2.10.1 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-2.6.31-23-generic-pae-i686-with-debian-squeeze-sid platform.architecture(): ('32bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 8 Memory total: 25,405,636,608 Memory free: 20,305,633,280 import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Å

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Calculating Bijvoet difference Fourier map
by John Rose 08 Mar '12

08 Mar '12

Hi, I am some what new to PHENIX and using the Mac GUI. I want to compute a Bijvoet difference Fourier map. Any help would be appreciated. John Rose

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autobuild omit map as Fo-Fc
by Ursula Schulze-Gahmen 08 Mar '12

08 Mar '12

I calculated an omit-map for my model using the following command inpt: phenix.autobuild data=HKL2000+R.mtz model=ptefb_A4_refine_43.pdb omit_region_specification=omit_around_pdb omit_box_pdb_list=G_chain.pdb composite_omit_type=refine_omit maps_only=true I would like to display a 2Fo-Fc and Fo-Fc map but I cannot find the overall_best_refine_map_coeffs.mtz output file that should have these coefficients according to the manual. I only see the overall_best_denmod_map_coeffs.mtz file. Can somebody tell how to best get to an omit Fo-Fc or 2Fo-Fc map? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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bins in phenix.refine
by Jianghai Zhu 06 Mar '12

06 Mar '12

Hi, A colleague asked me a question if phenix.refine can use user-input resolution bins for R and Rfree calculation. I am not sure if such parameters exist. -- Jianghai

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where is the fo-fc omit map?
by Yu, Hongjun 06 Mar '12

06 Mar '12

hello, It is so good that phenix can caculate sa-omit map so easily. But I am new to this. When I finish caculating, I can only get acess to 2fo-fc map whe I use coot to open the file: resolve_composite_map.mtz . How can I open the fo-fc omit map? I notice this from phenix.autobuild manual page "Note 1: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz". I don't understand this because the omit_regin.mtz seem to be the omit box I specify. Is this correlated with my problem? Any advice is appreciated. Thank you in advance! Sincerely, Hongjun

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phenix.get_cc_mtz_pdb but allow for atom selections.
by Francis E Reyes 06 Mar '12

06 Mar '12

It'd be wonderful to pass in an atom selection (say backbone, or ligand or what have you) into phenix.get_cc_mtz_pdb . Is this functionality available in some other phenix util? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Batch conversion
by Theresa H 06 Mar '12

06 Mar '12

Hi all How can I use ADXV to batch conversion of diffraction image to tiff format? Would like to put about 20 of them in Powerpoint slides. Thank you. Theresa

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fwd: Reminder: CCP4 summer school at APS, in USA
by Nathaniel Echols 02 Mar '12

02 Mar '12

FYI, Paul Adams and Tom Terwilliger will both be presenting at this workshop. ---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "'phenixbb(a)phenix-online.org'" <phenixbb(a)phenix-online.org> Cc: Date: Fri, 2 Mar 2012 14:22:53 -0600 Subject: Reminder: CCP4 summer school at APS, in USA Dear Colleagues, This is a reminder that the deadline for applications for the 5th annual CCP4 Summer School “From data collection to structure refinement and beyond” is April 17, 2012. The school will take place from June 19 through June 26, 2012 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (The program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2012/index.php The school will include data collection, processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: Sanishvili, Ruslan Sent: Monday, December 19, 2011 11:39 AM To: 'phenixbb(a)phenix-online.org' Subject: Annual CCP4 summer school in USA, at APS, June 19-26 Dear Colleagues, We are pleased to announce the fifth annual CCP4 summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2012/ Title: "CCP4 school: From data collection to structure refinement and beyond" Dates: June 19 to 26. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections – lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is April 17. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2012/ Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers will arrange economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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xtriage output
by wtempel 02 Mar '12

02 Mar '12

Hello, this question is about the summary of xtriage output. I submitted merged scalepack intensity in space group P3. From scaling, the apparent point group is P622. H-tests for all three applicable twin laws indicate twin ratios around 45%. Does this merely indicate underestimated symmetry? STDOUT ends with this nugget: <stdout> The results of the L-test indicate that the intensity statistics Show more centric character than is expected for acentric data. </stdout> My questions: 1. What if anything should I infer about twinning from this last sentence? 2. What other data defects could this sentence indicate? Many thanks, Wolfram Tempel

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DEN refinement under phenix
by Melania Strycharska 02 Mar '12

02 Mar '12

Hi All, I was wondering whether anybody has successfully run the DEN refinement under phenix yet. I am having some problems with my scripts stalling without any error messages. What sort of reference models do people use? The following issues I am not quite clear on: - if I don't have a reference model should I call on my current pdb where the script calls for a reference model? - is it ok to use a single domain as a reference model or is it not enough to get the whole protein refined? - is it possible to use more than one reference model; in a case where I had structures of each domain solved separately? - can a reference model be a different protein or does it have to have the same sequence? Thanks a lot!

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Rfree refuse to come down
by #HEW KAI LI KELLY# 02 Mar '12

02 Mar '12

HI, I have a few questions about a dataset that I am working on currently. So I ran Xtraige and it tells me that other than pseudoNCS, there is no other problems like twinning etc. And then I used autoMR and Phaser from Phenix to run molecular replacement with a the structure of the same protein (but that is with DNA bound). The TFZ is more than 9 after from both the runs. Autobuild managed to build the 4 molecules in my ASU (Rfactor/Rfree = 28/32 for a resolution of 2.4A). But because there are some clashes and outliers in the Ramachandran Plot etc, I started to manually refine them in coot. In addition, there is a loop that is unable to fit into the density, so I chopped about 10 residues off each molecule in the ASU. However, as I started to refine the model from AutoBuild, my Rfree begins to climb. So currently, I am at Rfactor/Rfree=27/36. I don't know if there is anything wrong with I had done. So many thanks in advance for your advices on this!! Warmest Regards, Kelly Hew Nanyang Technogical University School of Biological Sciences Division of Structural Biology & Biochemistry Address : #07-01, IMCB, 61 Biopolis Drive, Proteos, Singapore 138673 Telephone (O): +65 65869673 Telephone (HP): +65 98713553

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