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International Conference on Structural Genomics - Structural Life Science, Sapporo, Japan, July 29-Aug 1, 2013
by Terwilliger, Thomas C 18 Mar '13

18 Mar '13

Dear Colleagues: On behalf of the organizing committee of the International Conference on Structural Genomics 2013 – Structural Life Science – (ICSG2013-SLS), we cordially welcome you to the conference, to be held in Sapporo, Hokkaido, Japan, July 29th – August 1st, 2013. ICSG2013-SLS is intended to provide an overview for the most recent developments in Structural Genomics and its impact on research in biology, medicine and disease, and to foster international collaboration among researchers. You can see all the details of the conference at: http://www.c-linkage.co.jp/ICSG2013 . Registration for the conference is now open. The scientific topics covered in ICSG2013-SLS include the wider life science research fields with particular attention to drug discovery (small molecules and biopharmaceuticals), biotechnology and industrial issues while keeping strength in the high-throughput technologies and integration of hybrid methods. These technologies are now leading to the new field of “Structural Life Science”. ICSG2-13-SLS is partially supported by the Grant-in-Aid for Scientific Research on Innovative Areas; “Structural Cell Biology”, “Intrinsically Disordered Protein” and “Transient Macromolecular Complexes”, from Ministry of Education, Culture, Sports, Science and Technology (MEXT) . In order to widen the opportunity to young and enthusiastic fellows to study more, we have organized several satellite workshops before ICSG2013- SLS. The topics will include “Small molecule screening”, “Automation of X-ray Structure Determination”, “Cell-free Protein Production”, “Automated NMR methods”, "Eukaryotic expression", “Interaction analyses" and "Bioinformatics”. We hope you also find the satellite workshops are informative and productive. The conference will be held in Keio Plaza Hotel Sapporo, in walking distance of Hokkaido University's main campus and Sapporo station. The summer in Sapporo is a great time to stay and enjoy the cool summer night of Japan. We are looking forward to welcoming you to Sapporo in the summer of 2013. Sincerely yours, Katsumi Maenaka, Ph.D. Chair, International Conference on Structural Genomics 2013 -Structural Life Science- (ICSG2013-SLS) Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Japan Soichi Wakatsuki Chair of Program Committee, ICSG2013-SLS Photon Science, SLAC National Accelerator Laboratory Department of Structural Biology School of Medicine Stanford University

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MR_rosetta and disulphides
by Morten Groftehauge 17 Mar '13

17 Mar '13

Hi guys, Phenix version 1323 Rosetta version 3.4 I try to run phenix.mr_rosetta rosetta_command="-MR::disulf 129:411 228:281 279-615" mr_rosetta_228.eff but I get the following error in rebuild.log ERROR: Option matching -MR:disulf not found in command line top-level context I lifted the rosetta_command directly from the Version Documentation. Any clues as to why this doesn't work? Sincerely, -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Tutorial of low resolution data?
by 李翔 16 Mar '13

16 Mar '13

Hi everyone, I will work on some low resolution data but have very little experience. (Data are about 4 A to 8 A) Does anyone know where I could find a tutorial for low resolution data please? It is best to work with Phenix, other software is fine. MIR or SAD or MR method will be appreciated and it is very helpful if the tutorial can talk about some details of the data processing. Cheers, Frank

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Phenix DEN-twin-refinement
by Ethayathulla A.S 14 Mar '13

14 Mar '13

hi all I want to do DEN twin-refinement using phenix. For my data phenix.DEN works better than CNS DEN. I want to DEN with twinning. Is there script for adding twinning operator for DEN refinement in phenix phenix.den_refine model.pdb data.mtz den.reference_file=reference.pdb Thank you Abdul --

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Re: [phenixbb] problems installing latest phenix on mac osx lion
by Alejandro Buschiazzo 14 Mar '13

14 Mar '13

Thanks Nat! read your message a bit later (I think I need to change from the digest format, so I receive each message as it comes), looking at http://phenix-online.org/pipermail/phenixbb/2013-March/thread.html Actually, your suggestion worked all right. (and by sourcing the phenix_env.sh as you point out, it's actually the same as the command line -installer of course) Don't know why the errors appeared before, but in any case, now it's running fine. Thank you for your help Alejandro > Not sure what's going on here - I will check it out today. There's > one more option however that should be the safest: did you try the > graphical installer yet? The destination can't be changed, but you > can still use the command line if you want by doing this: > > source /Applications/PHENIX-1.8.2-1309/Contents/phenix-1.8.2-1309/phenix_env.sh > > (or the csh equivalent) > > But I will see if there's an explanation for these errors. > > -Nat On Tue, Mar 12, 2013 at 4:26 AM, Alejandro Buschiazzo <alebus at pasteur.edu.uy <http://phenix-online.org/mailman/listinfo/phenixbb>> wrote: >/ I 'm trying to install phenix 1.8.2-1309 on a Macbook Pro (os x 10.7.5). />/ />/ First tried the binary installer proposed (which is indicated for os x />/ 10.6.7) />/ It didn't work, ending with "fix_mac_python: caught error - exiting." />/ />/ I spotted in the bb that this could've happened because the downloaded />/ installer was somehow corrupted, tried downloading it again, but same />/ result. />/ />/ Tried then the source installer: everything OK - except for wxPython, giving />/ this error />/ />/ WXPYTHON: />/ Using wxOSX_Cocoa build of wxPython 2.9 alpha version />/ />/ building wxPython-src-2.9.4.1 />/ ERROR: installation of wxosx_cocoa failed />/ />/ ERROR: installation of wxpython failed />/ />/ ...now I can work with command lines, but the GUI won't work of course. />/ />/ Your help is appreciated />/ />/ Alejandro />/ />/ />/ -- />/ 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/ -- 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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Fwd: 4th Edition of the ISBC2013
by Nathaniel Echols 14 Mar '13

14 Mar '13

---------- Forwarded message ---------- From: Jose A. Gavira <gavirius(a)gmail.com> Date: Thu, Mar 14, 2013 at 11:20 AM Subject: 4th Edition of the ISBC2013 Dear Colleague, The Laboratory of Crystallographic Studies is pleased to announce the 4th International School on Biological Crystallization (ISBC2013), to be held in Granada (Spain) during May 26-31, 2013. ISBC2013 is intended for postgraduate/postdoctoral students and research scientists from industrial and academic backgrounds. The International School will provide five days of lectures, posters and practical demonstrations focused on the fundamentals of crystallization from solution and their applications to the field of crystallization of biological materials, including biological macromolecules, biominerals and biomimetic materials. One day will be fully devoted to case studies on the crystallization of membrane proteins, viruses and large macromolecular complexes. For more information, please visit http://www.isbcgranada.org/<http://www.linkedin.com/redirect?url=http%3A%2F%2Fwww%2Eisbcgranada%2Eorg%2…> . Best regards, ISBC2103 Organizing Committee --- Gavi http://isbcgranada.org/

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problems installing latest phenix on mac osx lion
by Alejandro Buschiazzo 12 Mar '13

12 Mar '13

Hello, I 'm trying to install phenix 1.8.2-1309 on a Macbook Pro (os x 10.7.5). First tried the binary installer proposed (which is indicated for os x 10.6.7) It didn't work, ending with "fix_mac_python: caught error - exiting." I spotted in the bb that this could've happened because the downloaded installer was somehow corrupted, tried downloading it again, but same result. Tried then the source installer: everything OK - except for wxPython, giving this error > WXPYTHON: > Using wxOSX_Cocoa build of wxPython 2.9 alpha version > > building wxPython-src-2.9.4.1 > ERROR: installation of wxosx_cocoa failed > > ERROR: installation of wxpython failed ...now I can work with command lines, but the GUI won't work of course. Your help is appreciated Alejandro -- 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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GUI display items
by Luca Pellegrini 09 Mar '13

09 Mar '13

Hello, Is there a way to change/select the column items displayed in the PHENIX home window, under the 'Job history' tab? At the moment, mine shows: ID/Program/Date/Job title or directory/R-free. I would like to add things like the Overall score from MolProbity etc. I looked under Preferences but couldn't find anything. Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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fwd: EMBO 2013 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 10 - 14 June 2013
by Nathaniel Echols 09 Mar '13

09 Mar '13

(Note that the registration deadline is tomorrow.) ---------- Forwarded message ---------- From: Daniele de Sanctis <desancti(a)esrf.fr> To: phenixbb(a)phenix-online.org Date: Sat, 9 Mar 2013 12:51:54 +0100 Subject: EMBO 2013 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 10 - 14 June 2013 DEADLINE Tomorrow COURSE ANNOUNCEMENT EMBO 2013 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 10 - 14 June 2013 The EMBO 2013 Practical Course on Exploiting Anomalous Scattering in Macromolecular Structure Determination will be hosted by the ESRF in Grenoble, France from 10 to 14, June 2013. The course aims to impart the theoretical and practical basis for the 3-dimensional structure determination of bio-macromolecules using Anomalous Dispersion techniques (SAD & MAD) to young scientists who intend to apply these methods in macromolecular crystallography. Through a series of lectures, software demonstrations, practicals on the ESRF beamlines and tutorials, participants will get insights into all aspects of the structure determination process including beamline instrumentation, data collection and processing, heavy atom substructure determination, phasing and model building. There will also be sessions focusing on automated structure solution procedures and newer methods. Additional sessions will include presentations of distinguished structures solved with these techniques. The number of participants is limited to 20 and the deadline for application is March 10th, 2013. Additional information, course programme and instructions to apply to the course can be found in the course webpages: http://events.embo.org/13-crystallography/ Confirmed invited speakers include: Andreas Bracher, Kay Diederichs, Rita Giordano, Adrian Goldman, Wolfgang Kabsch, Gordon Leonard, Airlie McCoy, Sean McSweeney, Christoph Müller-Dieckmann, Max Nanao, Alexander Popov, Harry Powell, Thomas Terwilliger, Andrew Thompson, Isabel Uson, Clemens Vonhrein -- ἀρετή --------------------------------------- Daniele de Sanctis, PhD Structural Biology Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

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map woes from refine
by Machius, Mischa Christian 08 Mar '13

08 Mar '13

Y'all, Recently, I've run into an issue with the maps from refine. All during the refinement cycles, the autoupdated maps in the associated coot window look great as refinement progresses. However, the final maps look horrible; completely chopped up. It's not a matter of contouring levels; it's essentially unrecognizable, and phenix acknowledges that by stating very low correlation coefficients at the end of the log file. I have downloaded the latest builds in an attempt to address B-value issues that were recently discussed and that I am (still) struggling with. The map issue happens with all of them. Is it possible that there is some crossfire from different versions, or any other reason? Any help appreciated. Cheers, MM

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selection of different residue ranges for a NCS group
by Andres PALENCIA 07 Mar '13

07 Mar '13

Dear All, I am trying to select different regions of the same protein to be included in the same NCS group before refinement. This correspond to the core of a protein. Additionally, I would define other NCS groups for external domains. I have 4 protein/RNA complexes in the asu, P1. Here are the residue ranges for the NCS group corresponding to the core of the protein (invariant): Chain A and resseq: 1:156, 188-227, 413:568, 629:794 this should be the reference group, to match the same region in the other 3 monomers (C, E. G). Other NCS groups will include the RNA, as well as other external domains: Chain B and resseq: 1: 87 This is the RNA molecule, that should match the other 3 monomers (D, F, H) Chain A resseq: 157:187 this is a external domain, to match the other protein monomer (C, E, G) and so on.... for other external domain I have seen that there is the possibility to use user-defined NCS groups, by using: * ncs_groups.params * or modifying the GUI by editing the atom selection For the external domains I think is easy as the syntax is only one line, however for the core of the protein I do not manage to select properly the different residue ranges. Could anybody please help on that? what would be the easiest way to do that? Can I for example creat a ncs_groups.params file and add it to phenix.refine in the GUI? Thanks in advance, Andres

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map scaling: sigma or volume scaled
by Edward A. Berry 06 Mar '13

06 Mar '13

map scaling can be defined: sigma or volume scaled Maybe another dumb question, but what is volume scaling? For 2mFo-DFc and mFo-DFc maps. Thanks, Ed

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quick clashlist or molprobity in batch mode
by jan 06 Mar '13

06 Mar '13

Hi all, I want to analyze a whole bunch of structures with molprobity, and I am looking for a convenient way to do this. phenix.quick_clashlist seems to be a handy tool. However, when I use the following command line: "phenix.quick_clashlist model=mypdb.pdb" ... the output tells me: # run_clashlist # # Run reduce and molprobity # type phenix.run_clashlist: --help for help Parameters used: run_clashlist { model = "4iuj.pdb" build = True summary_file = None output_file = None temp_dir = None remove_temp_dir = None verbose = False raise_sorry = False debug = False dry_run = True } ************************************************ 'str' object has no attribute '_anchor' ************************************************ Any ideas what I need to do differently? thanks, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

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Using Phenix Refine for Hypothetical Models
by Sam Stampfer 06 Mar '13

06 Mar '13

Dear Phenix Community, Is it possible to use phenix.refine to do simulated annealing and energy minimization of a hypothetical model? I am currently using pyrosetta relax for minimization; however, my hypothetical model is based on a homologous protein whose structure is a crystallographic trimer. I would like to preserve my model's symmetry, which I know is possible in phenix.refine but not in pyrosetta (the symmetry controls are only supported in regular rosetta, as far as I know). Is there a way to have phenix ignore x-ray data and just do energy minimization functions? How would I go about doing that? Would I need a file containing fake/dummy x-ray data? Thanks for your help! -Sam Stampfer

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Fwd: FINAL REMINDER: ALS Call for General User Proposals - DEADLINE March 6 2013
by Banumathi Sankaran 05 Mar '13

05 Mar '13

Dear Users, I am forwarding the reminder mail from ALS to submit your proposal for the CC time and general user time at ALS. Please submit your proposals before time. Thanks Banu FINAL REMINDER: CALL FOR GENERAL USER PROPOSALS AT THE ALS The User Services Office is accepting General User Proposals from scientists who wish to conduct research at the ALS in the next cycle. PROPOSAL SUBMISSION DEADLINE cycle: 2013-2 August-December Deadline: March 6, 2013 NEW PROPOSALS Please follow the instructions for proposal submission at: http://www-als.lbl.gov/index.php/user-information/user-guide/58.html BEAM TIME REQUEST for an ACTIVE PROPOSAL Proposals remain active for two years (up to four cycles), but beam time is only allocated if a beamtime request is made each cycle. After two years the proposal expires and a new proposal must be submitted. If you have an eligible active proposal you will already have received an email from us which includes your login number and password. PUBLICATION REMINDER The proposal form now includes a section on publications from previous ALS work. Please make sure your publications are entered into our database: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PublicationSearch.shtml/Initialize If you have questions, please feel free to contact me. Cheers, Clyde Lewis Proposal Coordinator ALS

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Memory and CPU usage
by Jon Agirre 05 Mar '13

05 Mar '13

Dear community, I'm planning on buying a new macbook for my first abroad postdoc venture, and I'm currently trying decide what amount of RAM & CPU to choose. My question is a little bit intricate: is there any rule of thumb to estimate the needed RAM versus the number of input atoms for any particular refinement type? I'm planning on tackling some big (18,000 residues/asu) refinements but I don't have any estimation as to how many GBs of RAM they might require. The maximum amount of RAM I can install is 16GB, but it is a non-standard configuration that might void Apple's warranty. About the CPU: how scalable are typical phenix processes? Would it be sensible to invest in a quad-core machine with HT? In this particular case, and since HT would present 8 logical cores, would I get any speed up from launching phenix tasks configured for 8 processors instead of 4? Thanks in advance! Jon

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Unusually low B factors with phenix 1.8, but not with phenix 1.7 (data set has ice rings)
by Oliv Eidam 04 Mar '13

04 Mar '13

Hi, I would like to continue the B-factor discussion started by Demetres D. Leonidas on Nov 2, 2012 on CCP4BB: http://www.mail-archive.com/[email protected]/msg29012.html I make the same observations like Demetres and Mingzhu Wang: unusually low B-factors when refining with Phenix 1.8-1069 and 1.8.1-1168, but not with Phenix 1.7.1-743. In numbers: the average B-factor is 10 A2 but it should be 20 A2 (based on Wilson B and similar structures). A few atoms (~20) have Bf = 0.00. The following is important: I refined dozens of similar structures without that problem and I observe this phenomenon only for a single data set. That specific data set is different because 1) I excluded regions with ice rings in XDS and 2) I limited the resolution to 2.28 Angstroem, although the crystal diffracted to ~1.8 Angstroem. While the preparation of the data set might be questionable in itself, I would prefer that this would not be the topic of this thread. My questions are: What can I do to refine my structure with Phenix 1.8.X using this truncated data set? What causes the difference in average B-factor values between Phenix 1.7 and 1.8 for this data set? Your advice is much appreciated. Oliv On 11/04/12 19:21, mingzhu wang wrote: > Pavel, > > 1.8.1-1168 also has this problem. > > I found this problem existed with some dataset, but not all dataset. > > 1.8.1 give better map, so I built model with 1.8.1 map and go back to > 1.7.3 before I deposit the structure to PDB. > > When I compared the B factor from 1.8.x and 1.7.3, I found > B(1.7.3)=B(1.8.x)+Boverall(1.8.x). Perhaps this is the problem. > > > > 2012/11/3, Pavel Afonine<pafonine(a)gmail.com>: >> Joao, >> >> I am using the latest version of phenix 1.8.1-1168 >> >> >> 1.8.1-1168 should not have that "problem". >> >> If you suspect there is still a problem, you can send me the data and model >> files off list, explain what exactly the problem is, and I will have a look >> right away. >> >> FYI: there is Phenix mailing list for Phenix-specific questions, where I >> can also explain in great details the behavior with the B-factors you >> observe. >> >> All the best, >> Pavel >> -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email:[email protected]

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fwd: Reminder: CCP4 summer school at APS, USA
by Nathaniel Echols 04 Mar '13

04 Mar '13

---------- Forwarded message ---------- From: "Ruslan Sanishvili (Nukri)" <nukri(a)aps.anl.gov> To: phenixbb(a)phenix-online.org Date: Mon, 4 Mar 2013 16:14:43 -0600 (CST) Subject: Reminder: CCP4 summer school at APS, USA Dear Colleagues, This is a reminder that the deadline for applications for the 6th annual CCP4 Summer School “From data collection to structure refinement and beyond” is April 5, 2013. The school will take place from June 18 through June 26, 2013 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-2013/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. We hope to see you in June Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science 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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Bay Area and Beyond Phenix User Meeting (March 14th)
by Paul Adams 04 Mar '13

04 Mar '13

Dear Colleagues, On Thursday March 14th, a Bay Area and Beyond Phenix User Meeting will be held at Lawrence Berkeley Lab. During the workshop, the Phenix developers will give lectures on the latest developments and Phenix usage. Half of the user meeting will be in the form of informal hands on sessions, allowing participants to work with the developers. Participants are encouraged to bring their own (reduced) data to be used during hands on sessions, but tutorial data will also be available. We also recommend bringing a relatively recent laptop computer (any OS). Due to the highly interactive format of the meeting there will be space for approximately 20 participants. If I have missed any of your colleagues on this invitation please feel free to pass on the message. To apply, researchers should send a short summary email describing their level of expertise and motivation for attending the workshop to NEchols(a)lbl.gov and PDAdams(a)lbl.gov by Friday March 8th. Cheers, Paul -- 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.refine multiple twin laws?
by Kip Guja 03 Mar '13

03 Mar '13

Hi All, Is the newest version of Phenix capable of refinement with multiple twin laws (eg, tetartohedral twinning)? If so, any advice on input parameters, etc. would be greatly appreciated. Best wishes, Kip

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Re: [phenixbb] Magnesium or calcium
by Daniel Slade 02 Mar '13

02 Mar '13

So the resolution is 1.6 and I remember the B factor for mg at 16. I haven't checked the coordinating residues. It coordinates acidic residues, a backbone carbonyl and one water. I'm now leaning towards calcium as the other calciums have bonds distances similar to this one, but not nearly as high an affinity. Thanks

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Magnesium or calcium
by Daniel Slade 02 Mar '13

02 Mar '13

I have several structures that has multiple known calcium binding sites, and I found a new site that seems to accept calcium or magnesium. I say this because if a magnesium is put in the structure, the bond lengths are ~ 2.1. But if you put a calcium in it, they go to ~2.6. All of these refinements were done without ReadySet, which I recently used with metal restraints and it seemed to change the bond length of calcium to ~2.4. I'm a bit confused as to what to do here as either metal seems to be right. Worth noting, this is a very strong metal binding site that can't be removed with 10 mM EDTA. Any help here on how to figure this out which ion this is would be great. Thanks in advance Dan

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Re: [phenixbb] Magnesium or calcium
by Ed. Pozharski 02 Mar '13

02 Mar '13

Magnesium has fewer electrons. So if you place it and it's actually calcium you should see extra density and the B-factor will be unreasonably lower than surrounding atoms. Distances are less reliable at intermediate resolutions as they are largely controlled by restraints. Maybe. Assuming that you have 100% occupancy. -------- Original message -------- From: Daniel Slade <DSlade(a)scripps.edu> Date: To: phenixbb(a)phenix-online.org Subject: [phenixbb] Magnesium or calcium I have several structures that has multiple known calcium binding sites, and I found a new site that seems to accept calcium or magnesium. I say this because if a magnesium is put in the structure, the bond lengths are ~ 2.1. But if you put a calcium in it, they go to ~2.6. All of these refinements were done without ReadySet, which I recently used with metal restraints and it seemed to change the bond length of calcium to ~2.4. I'm a bit confused as to what to do here as either metal seems to be right. Worth noting, this is a very strong metal binding site that can't be removed with 10 mM EDTA. Any help here on how to figure this out which ion this is would be great. Thanks in advance Dan _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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question about reflection file tools behavior
by Michael Thompson 01 Mar '13

01 Mar '13

Hello All, I have a question about the behavior of the reflection file tools within the PHENIX GUI: I am trying to simply copy a set of FreeRFlags from a higher resolution dataset to a lower resolution dataset. The low-res dataset contains 35264 reflections in the original input mtz. The high-res set contains 43731 reflections. When I use the GUI to write a new mtz using the low-res amplitudes and the high-res FreeRFlags, the result is an mtz with 46323 reflections. I am confused about why the output has so many reflections, even more than the high res dataset? Also, I noticed that while both input mtz files have a low-res cutoff of 20A, the output mtz has a low-res cutoff around 75A. Can anyone please explain what is going on here? I would like my output file to have the same reflections as the input, and no more. I have noticed that the CCP4 program FreeRFlag seems to behave in a similar way, so my guess is that what is happening is a common procedure, but I'm at a loss for an explanation of why this is the case. Also, if there's a better way to implement what I am trying to do I'd be grateful to hear it (perhaps generate entirely new flags for both datasets using the same random seed?). Thanks for the help!! Mike -- 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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mr_rosetta fails after autobuild stage
by Huw Jenkins 01 Mar '13

01 Mar '13

Hi, I've been having some problems with mr_rosetta. All the regression tests run fine but when I run it on some real data it gets as far as the autobuilding stage and then fails with an error message. All I can find in the log files GROUP_OF_AUTOBUILD_1/RUN_FILE_1.log GROUP_OF_AUTOBUILD_1/RUN_FILE_2.log is ******************* ERROR ENDING *************** Failed to carry out autobuild ******************* ERROR ENDING *************** The autobuild jobs themselves seem to finish fine i.e the end of the log files in GROUP_OF_AUTOBUILD_1/RUN_1/AutoBuild_run_1_ and GROUP_OF_AUTOBUILD_1/RUN_2/AutoBuild_run_1_ has the tables of Rfactors per cycle and the list of citations with no indiction of any error. Is there anywhere else I should be looking for a more detailed error message? Thanks, Huw

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