- phenixbb - phenix-online.org

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 07 Mar '12

07 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 05 Mar '12

05 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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Fwd: Hi Res Model. Maybe its time to Include Hydrogens?
by Yuri 01 Mar '12

01 Mar '12

Sue: I am not sure they are being included... I have the option checked, but the R values and difference maps tell me otherwise Pavel: A bug? That would be consistent with the behavior I observe. Even when I enable refinement with hydrogens individual or riding, i see essentially no difference in maps or Rfree values. -- Yuri Pompeu

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Hi Res Model. Maybe its time to Include Hydrogens?
by Yuri 01 Mar '12

01 Mar '12

Dear users, I am refining a 400 aa protein with data out to 1.16 A (real data). I am almost finished with refinement. I have good geometry, complete model and ligands Rw 0.11 Rf 0.13. Difference maps seem to be asking for more. See attached screen shot.Both maps 2Fo-Fc (non-filled) and Fo-Fc are contoured at 3 sigma. How should I handle this? I have used hydrogens all along (riding). Thanks for your time -- Yuri Pompeu

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phenix.reciprocal_space_arrays question
by Michael Thompson 01 Mar '12

01 Mar '12

Hi All, I have a very simple question about phenix.reciprocal_space_arrays. I apologize if this is obvious, but I could not find any info in the documentation or the bb archives. I just want to make sure that I am actually doing what I think I am doing. If I provide phenix.reciprocal_space_arrays with an .mtz file containing Fobs and a .pdb file for which I would like to calculate Fmodel and PHImodel, will the resulting Fmodel (and Fcalc, Fmask, Fbulk, etc.) be scaled to the Fobs from the input .mtz? Thanks for the help! Mike T. -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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BCA/CCP4 Summer School 2012
by Airlie McCoy 01 Mar '12

01 Mar '12

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 BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new to crystallography. Its dual aims are to provide comprehensive training in crystallography and to promote best practise within the British crystallographic community. The lectures cover the gamut of techniques required for a structure solution, from protein expression through to structure validation. Intensively supervised computer tutorials enable students to relate the theory presented in the lectures to practice. Although CCP4 programs will primarily be used in these tutorials, the aim will be to approach crystallographic questions in a software-agnostic manner. There will also be a crystal manipulation and cooling workshop. (Note that the course is scheduled during Diamond synchrotron downtime, so there will not be active data collection at the Diamond beamlines.) For more information on eligibility, cost, and applications 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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NCS-averaged and superposed maps
by Mullins, Elwood 29 Feb '12

29 Feb '12

Is it possible to both NCS-average and superpose maps? I can do one or the other easily enough from the command line (phenix.ncs_average) and the GUI (Superpose maps). Unfortunately, both programs require the input to be an mtz file but output ccp4-style maps. I don't see a way to do this sequentially. Is there some other method that would allow me to perform both operations? Thanks, Elwood =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Elwood A. Mullins Ph.D. Candidate Department of Chemistry Washington University in St. Louis Campus Box 1134 One Brookings Drive Saint Louis, MO 63130-4899 Email: elwood.mullins(a)wustl.edu Tel: (765) 496-6814 Fax: (765) 494-7897 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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R-free flags
by 刘世恒 29 Feb '12

29 Feb '12

Hi, According to the phenix documentation, phenix.refine generates free R that are evenly distributed over the resolution, making sure that relatively thin resolution bins receive enough of reflections. The default behavior is to flag 5% of reflections up to a maximum of 2000. However,in some high-resolution structure, the percent for R-free test set which was generated by phenix.refine might be smaller than 1%， and it was a small percentage. Are there anticles related to the generation of R-free flag by phenix? Sincerely yours, Shiheng Liu

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adding solvents other than water
by Subhani Bandara 28 Feb '12

28 Feb '12

Hi all, How can I identify atoms like Na+, K+ in the map, from the positive density. Also can I add solvents like MPD and Tris buffer if any. Is there a specific way or do I have to run ligand fit. Is there any material I can read on this. Thanks in advance. Subhani

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Fixing ligand position in refine
by Christopher Wanty 27 Feb '12

27 Feb '12

Hi, I have a problem with a phosphate moving out of position during refinement. The complication is that there is an existing phosphate in the same location as the one I'm trying to place, but the existing one is part of a modified residue, and there is clearly density for the alternative conformation of the phosphate, but it is also clearly not still bound to the residue. How do I make sure that the phosphate does not move away from where it should be? Attached image show the phosphate more or less where I want it, and you should be able to see where the existing phosphate is attached to the residue. The large red density blob is where phenix.refine tried to put the phosphate last time. 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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