- phenixbb - phenix-online.org

is derivative data useful for looking for the missing part of the model?
by fn1＠rice.edu 16 Jun '10

16 Jun '10

Hi everyone, I got a partial model, consisting of 80% of the whole molecule, from the molecular replacement. The native data reflects to 2.3 A, and now the R/Rfree= 0.22/0.28. My problem is that the missing part of the model is important for us, but there is not any density for this region now. Meantime, we have several heavy atom derivative data. My question is that if refine the model against the derivative data, will the heavy atom appear in the difference map if existing? Any suggestions on how to use the derivative data to locate the missing part of model? Thanks in advance! Regards, Fengyun

3 4

Re: [phenixbb] input sharp phases into phenix.autosol
by Thomas C. Terwilliger 15 Jun '10

15 Jun '10

Hi Michael, If I understand correctly, you want to take a file that has experimental phases, density modify it, and autobuild a model. Plus you want to take the inverse hand of the phases and do the same thing. For the first part you have two easy options: phenix.autobuild my_exptl_phases.mtz my_seq.dat ha_file=my_ha_file phenix.build_model my_exptl_phases.mtz my_seq.dat ha_file=my_ha_file These do more or less the same thing, but build_model is a lot faster (but not quite as good), and requires version 1.6.2-242 or higher. For phases from sharp, you will want to specify the columns of data to be used for FP SIGFP PHIB FOM HLA HLB HLC HLD for each method above. (The way to specify these are different in the two methods. For autobuild you just list the column labels to be used for the above items with labels="myFP mySIGFP myPHIB myFOM myHLA myHLB myHLC myHLD", and for build_model you specify a regular labin line: labin="FP=myFP SIGFP=mySIGFP...etc" For the second part, flipping the hand of a file with experimental phases...I am not sure if we have a tool for that. Perhaps someone else can comment. All best, Tom T >> Hi, >> >> I hope what I want to do is not considered a crime :-) Is there a way to >> input phases e.i. from sharp into phenix.autosol (preferably the command >> line version) to run resolve with both hands and autobuild for a SAD or >> SIRAS case? >> >> Thanks! >> Michael >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

4 3

input sharp phases into phenix.autosol
by Michael Hothorn 14 Jun '10

14 Jun '10

Hi, I hope what I want to do is not considered a crime :-) Is there a way to input phases e.i. from sharp into phenix.autosol (preferably the command line version) to run resolve with both hands and autobuild for a SAD or SIRAS case? Thanks! Michael

1 0

Diffraction Methods GRC, Registration deadline is 27th June
by andrew＠mrc-lmb.cam.ac.uk 12 Jun '10

12 Jun '10

The biannual Gordon Conference on Diffraction Methods in Structural Biology will be held at Bates College in Lewiston, Maine from 18-23rd July. The program covers all aspects of macromolecular structure solution from crystallization to structure solution and refinement and includes sessions on complementary techniques and the potential of free electron lasers. Many of the leading methods developers will be present and the format of the meeting, with free afternoons, provides ample opportunities for informal discussions. The registration deadline is 27th June, so please apply soon ! ========================================================================= Limited funds are available to support new student and postdoctoral applications, contact andrew(a)mrc-lmb.cam.ac.uk for details. ========================================================================= Further details, including a full program and details on the application procedure can be obtained from: http://www.grc.org/programs.aspx?year=2010&program=diffrac We hope to see you there ! Andrew Leslie (Chair) & Ana Gonzalez (Vice Chair) Outline Program Diffraction Methods in Structural Biology, 18-23rd July 2010, Bates College, Lewiston, Maine Sunday pm: Macromolecular Structures, Pushing the boundaries Discussion leader: Michael Rossmann 1. ABC Transporters: Doug Rees 2. The Spliceosome : Kyoshi Nagai Monday am: Crystallisation and the diffraction experiment Discussion leader: TBA 1. Nanolitre crystallisation: Seth Harris 2. Twinning and disorder: Todd Yeates 3. Simulating the diffraction experiment: James Holton 4. Microcrystallography: Gwyndaf Evans Monday pm: Radiation damage and data collection strategies Discussion leader: Vivian Stojanoff 1. Radiation damage, experimental: TBA 2. Microbeams: Yanhui Zou 3. Testing data collection strategies with the Pilatus: Marcus Mueller Tues am: Synchrotron developments and automated data processing Discussion leader: Thomas Schneider 1. Synchrotrons, latest developments: Sean Mc Sweeney 2. Synchrotrons, latest developments: Janet Smith 3. Data processing with Xia2/CHEF: Graeme Winter 4. Data processing with AUTOPROC: Clemens Vonrhein Tues pm: Complementary techniques Discussion leader: Ana Gonzales 1. Electron tomography: Sriram Subramaniam 2. SAXS: Hiro Tsuruta 3. Spectroscopy: Carrie Wilmot Weds am: Structure solution and refinement Discussion leader: Paul Adams 1. SAD Phasing: Randy Read 2. Molecular replacement with BALBES: Garib Murshudov 3. PHENIX: Tom Terwilliger 4. TLS: Ethan Merritt Weds pm: Challenging problems/Membrane Proteins Discussion leader: TBC 1. Using cubic lipidic phase: Martin Caffrey 2. Membrane Proteins: Stephen White 3. Heterogeneity, low solubility and low resolution: structural pursuit on the ternary Myddosome complex in Toll-like receptor signaling: Hao Wu Thurs am: Selected Posters and Map improvement and Model building Discussion leader: Tassos Perrakis 1. COOT: Paul Emsley 2. Modelling nucleic acids: Johan Hattne Thursday pm: Future Methods, FELs, Diffraction imaging Discussion leader: Ed Lattman 1. Opportunities fof membrane protein analysis with FELs: Petra Fromme 2. Single particle imaging with pulsed hard Xray lasers: Anton Barty 3. Femtosecond nanocrystallography of membrane proteins using LCSL: John Spence

1 0

Job Openings: Industrial Post Doc - Structure Based Drug Design Method R&D
by Lance Westerhoff 11 Jun '10

11 Jun '10

Hello All- Good news! We have the following new position available. We are particularly interested in folks who have experience with xray refinement method research and development, so I figured this list would probably be a good fit. Please contact me if you know of anyone who might be interested: ================= Contact: Dr. Lance M Westerhoff - careers(a)quantumbioinc.com Based at: QuantumBio Inc., 200 Innovation Boulevard, State College, PA 16803 On the Web: http://www.quantumbioinc.com/careers/ Job Purpose: Beginning immediately, QuantumBio Inc, headquartered adjacent to The Pennsylvania State University in State College, PA, is in need of a post doctoral computational Biochemist/Chemist interested in continuing his or her career within a dynamic, small-company environment. Under the direction of Dr. Lance M. Westerhoff, General Manager of QuantumBio, the successful candidate will work with both academic and industrial partners to help transition and validate the novel, quantum mechanically based structure-based drug discovery technologies recently developed in the academic laboratory of Dr. Kenneth M. Merz Jr. to QuantumBios product line. The successful candidate will be integral to this project and will focus his or her efforts on the research and software development aspects necessary to validate and deploy this novel technology across the pharmaceutical industry. The position requires the candidate to have a Ph.D. in Chemistry, Biochemistry, or related field along with experience with the methods and software in the field. Due to the limited number of new work visas available, only American citizens or candidates with valid work permits will be considered at this time. A willingness to publish is required, and experience with C++, high performance programming, or xray refinement methods is a plus. Opportunities for advancement may be available through additional SBIR/STTR-style projects, and industry-supported collaborations. Further, in addition to the research and development duties of the project, the position will afford the successful candidate with access to and experience with QuantumBio's industry partners including a number of pharmaceutical, biotech, and computational firms. To apply, submit cover letter, CV, and one or two representative publications to the Contact above. About QuantumBio: QuantumBio Inc is accelerating drug discovery efforts by providing pharmaceutical, biotechnology companies and life science research organizations with a next generation of Computer-Assisted Drug Design (CADD) and Computer-Assisted Molecular Modeling (CAMM) solutions based on the increased accuracy and power of quantum mechanics. These solutions include a number of options tailored to each customers specific requirements including software licensing, services, and customization. See http://www.quantumbioinc.com/ for more! ================= Thank you for your time! -Lance ____________________ Lance M. Westerhoff, Ph.D. General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909

1 0

large coordinate and map shift after simulated annealing
by fn1＠rice.edu 11 Jun '10

11 Jun '10

Hi everyone, I am wondering why large coordinate shift could happen after simulated annealing (no rigid body refinement). Although it helps decreasing R values, it looks like the whole molecule shifts together by about 3 A. Is this normal? I read a post in previous phenixbb, but I still not understand it. Thank you very much! Regards, Fengyun

3 4

Persistant high average B-factor.
by Joseph Brock 10 Jun '10

10 Jun '10

Dear Phenix users, I am currently using version 1.6.1-353 and I'm working on a 1.7A structure that has refined quite well using Individual_sites+individual_adp(isotropic)+occupanices+TLS: Final R-work = 0.1776, R-free = 0.2262 However, I noticed that the average B-factor reported by polygon with these settings was quite high ( < 0.1 of other structures with a similar resolution). Discovering I could not change the value of wxu_scale when using individual_adp+TLS, I went about trying to reduce the average B using the method described here: http://phenix-online.org/pipermail/phenixbb/2007-September/000511.html However, I still can't seem to reduce the average B-factor. I've just done a refinement with the following non-default (extreme) target weight settings: target_weights { wxc_scale = 1.5 fix_wxc = 2 fix_wxu = 0.1 (wxu_scale = 1) But if anything, reducing wxu to such low values makes the avergae B-even higher while concuretnly making the gap between R-values much worse: Final R-work = 0.1602, R-free = 0.2457 This suggests to me that I'm obviously over fitting the data but I'm at a loss on how to proceed. Should i just accept that the automatic scaling used for Phenix TLS wxu is doing a good job and that my structure actually does have an unusually high avergae B? I'm fitting two ligands into density, which is at several places ambiguous, so I would like the most unbiased difference density possible. Many thanks in advance, Joe. _________________________________________________________________ New, Used, Demo, Dealer or Private? Find it at CarPoint.com.au http://clk.atdmt.com/NMN/go/206222968/direct/01/

3 3

Autobuild error message, please help!!!
by 신인철 10 Jun '10

10 Jun '10

Hi, everyone I have a problem in running phenix.automr I started AutoMR with the command: ---------------------------------------------------------------------------- ----- phenix.automr build=True data=ZZZZZZ_H-Nat_x22_P3221_from_P321.sca \ coords='1_SMsp.pdb 2_SMsp.pdb 3_SMsp.pdb 4_SMsp.pdb' \ identity='40 32 29 27' seq_file=ZZZZZZ_seq.dat input_seq_file=ZZZZZZ_seq.dat \ copies=4 ---------------------------------------------------------------------------- ------ AutoMR process seems to be done without any error but during autobuild process, I encounterd an error message as follows ---------------------------------------------------------------------------- ----- Re-using input PDB coordinates in build this cycle Running 3 parallel build jobs Standard build in parallel starting with refine.pdb_1 This is the first try at building this model Setting background=False as nproc=1 Try: 1 building 1 model Try: 2 building 1 model Try: 3 building 1 model Running up to 1 jobs in parallel... with total of 3 jobs Splitting work into 3 jobs and running 1 at a time with csh in /data1/disk02/icshin/UGI/MR/PHENIX_MR_8/AutoBuild_run_1_/TEMP0 Starting job 1... **************************************************************************** **** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /data1/disk02/icshin/ZZZ/MR/PHENIX_MR_8/AutoBuild_run_1_/TEMP0/RUN_FILE_1' icshin_com: No such file or directory. **************************************************************************** **** ---------------------------------------------------------------------------- ---------------------------------------------------------- What am I supposed to do? Please, help me! ------------------------------------------------------- Inchul Shin Structural Biology Lab. CALS. Seoul Nationl Univ.

2 1

how-to change resolve keywords using phenix.multi_crystal_average
by Bjørn Panyella Pedersen 09 Jun '10

09 Jun '10

Dear board I am doing a difficult case of density modification. I get good results using resolve after optimising some keywords. I now want to use multicrystal averaging. This works ok in dmmulti, but I would like to combine it with resolve. For this I have tried phenix.multi_crystal_average, which also runs phenix.resolve, but it uses default keywords for resolve, and I can't find documentation on how to change these keywords. Current maps from phenix.multi_crystal_average are worse that the optimized resolve maps, and I believe this is because of the default resolve settings. Is it possible to control resolve keywords using phenix.multi_crystal_average? And how can I do it? Thanks in advance -Bjørn -- Bjørn Panyella Pedersen, PhD Postdoc PUMPKIN, Centre for Membrane Pumps in Cells and Disease University of Aarhus, Dept. Molecular Biology Gustav Wieds Vej 10C DK-8000 Aarhus C, Denmark Phone: +45 89425261 E-mail: bjopp(a)bioxray.au.dk http://www.bioxray.au.dk

2 1

Re: [phenixbb] phenixbb Digest, Vol 55, Issue 7
by ak2197＠columbia.edu 08 Jun '10

08 Jun '10

Ok Alex Sent from my Verizon Wireless BlackBerry -----Original Message----- From: phenixbb-request(a)phenix-online.org Date: Mon, 07 Jun 2010 12:00:01 To: <phenixbb(a)phenix-online.org> Subject: phenixbb Digest, Vol 55, Issue 7 Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Robert Ng wants to stay in touch on LinkedIn (Robert Ng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 7 Jun 2010 08:57:29 -0700 (PDT) From: Robert Ng <ubi(a)ufl.edu> To: PHENIX list <phenixbb(a)phenix-online.org> Subject: [phenixbb] Robert Ng wants to stay in touch on LinkedIn Message-ID: <1916754023.4088196.1275926249246.JavaMail.app(a)ech3-cdn13.prod> Content-Type: text/plain; charset="utf-8" LinkedIn ------------ PHENIX, I'd like to add you to my professional network on LinkedIn. - Robert Ng Robert Ng Graduate Research Assistant at Department of Biochemistry and Biophysics Gainesville, Florida Area Confirm that you know Robert Ng https://www.linkedin.com/e/isd/1366202655/UCksvc1y/ ------ (c) 2010, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100607/f95d09c5/a…> ------------------------------ _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb End of phenixbb Digest, Vol 55, Issue 7 ***************************************

1 0