February 2011 - phenixbb - phenix-online.org

EMBO 2011 Practical Course - Exploiting Anomalous Scattering - ESRF - 6 - 10 June 2011
by Daniele de Sanctis 17 Feb '11

17 Feb '11

Deadline in 10 days!! DEADLINE TO APPLY FEBRUARY 28th COURSE ANNOUCEMENT EMBO 2011 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 6 - 10 June 2011 The EMBO 2011 Practical Course on Exploiting Anomalous Scattering in Macromolecular Structure Determination will be hosted by the ESRF in Grenoble, France from 6 to 10, June 2011. 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. Confirmed invited speakers include: G. Bunkoczi, A. Cameron, D. Chirgadze, Z. Dauter, P. Evans, M. Grininger, T. Gruene, W. Kabsch, S. Panjikar, N. Pannu, A. Popov, H. Powell, L. Sazanov, G. Sheldrick, T. Terwilliger, C. Vonrhein The number of participants is limited to 20 and the deadline for application is February 28th, 2011. Additional information, course programme and instructions to apply to the course can be found in the course webpages: http://cwp.embo.org/pc11-03/ -- ἀρετή --------------------------------------- Daniele de Sanctis, PhD Structural Biology Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

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At what percentage of saturated peaks is acceptable?
by Jason 17 Feb '11

17 Feb '11

Hi, I have a technical question that is not related to phenix, but I hope some expertise around may help me out. I am intending to increase the exposure time to gain some resolution. At the same time I do not want too many over exposed peak. The question comes to at what percentage of the saturated peaks is acceptable? Many thanks. ====================== Jason Structural Biology Department University of Pittsburgh ======================

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Fwd: Your message to phenixbb awaits moderator approval
by Francis E Reyes 16 Feb '11

16 Feb '11

I love how this bb denies large attachments.. I almost sent some sensitive data to the list! F Begin forwarded message: > From: phenixbb-bounces(a)phenix-online.org > Date: February 16, 2011 2:44:47 PM MST > To: francis.reyes(a)colorado.edu > Subject: Your message to phenixbb awaits moderator approval > > Your mail to 'phenixbb' with the subject > > Re: [phenixbb] phenix.refine: Sorry: Inappropriate value for > grid_step_factor: must be positive and non-zero. > > Is being held until the list moderator can review it for approval. > > The reason it is being held: > > Message body is too big: 932289 bytes with a limit of 40 KB > > Either the message will get posted to the list, or you will receive > notification of the moderator's decision. If you would like to cancel > this posting, please visit the following URL: > > http://phenix-online.org/mailman/confirm/phenixbb/83115d392956ed11e4b78631f… > --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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refinement with twinning
by alexander.singer＠utoronto.ca 16 Feb '11

16 Feb '11

Hi -- I have a twinned data set -- approximate twinning fraction of 0.4. I decided to try to try twinned refinement using phenix.refine in what would seem to be the appropriate manner -- from the "All Parameters" menu, I select twinning, hit "Run Xtriage now" on my mtz file, it gives me the input to the "Twin Law", I keep the rest of the values the same (gave no Anisotropy correction), hit OK, then run 3 cycles of refinement. The only thing is that the Rwork/Rfree values are really very good, almost too good to be true -- for my 1.7 A refinement, I have values of 12.4 and 14.8%, respectively for Rwork and Rfree. Is there anything that I may be doing wrong yielding R values which are artifically too low? Thanks for your help Alex -- Dr. Alex Singer C.H. Best Institute 112 College St. Room 70 University of Toronto Toronto, Canada, M5G 1L6 416-978-4033

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how to move one domain of a protein in respect to another?
by Tatyana Sysoeva 16 Feb '11

16 Feb '11

Dear all, I am working with a protein which form homooligomeric assembly. Each subunit of the assembly consists of 2 subdomains. I would like to create chimeras with the subdomains moved with respect to each other, keeping the linkers. I am wondering what would be the easiest way to do this? Any suggestions are welcome! Sincerely, Tanya

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phenix.refine: Sorry: Inappropriate value for grid_step_factor: must be positive and non-zero.
by Francis E Reyes 15 Feb '11

15 Feb '11

Hi all Refining a low res (~ 3.5A) structure using a reference structure that was solved to 3.0A. I get the following error right when the refinement starts =============================== refinement start ============================== Sorry: Inappropriate value for grid_step_factor: must be positive and non-zero. All instances of grid_step_factor in my .def are positive and non-zero (they should be defaults b/c I never changed them). Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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phenix.model_vs_data feature request
by Stephen Graham 15 Feb '11

15 Feb '11

Hi there, A simple feature request: Like most phenix programs, when run from the command line phenix.model_vs_data fails when it is passed an mtz file with multiple 'data' columns (i.e. Fs, F(+/-)s, Is). However, unlike say phenix.xtriage it doesn't tell you the list of possible column combinations and the correct keyword. Would it be possible to add this in? Thanks, Stephen -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638

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phenix.maps
by Jason 15 Feb '11

15 Feb '11

Hi everyone, I have noticed that the coefficient mtz file generated by phenix.maps can't not be loaded to coot (it can be read through the link in the GUI version once after process). I am using 1.7 version. Any suggestions? -- ====================== Jason Structural Biology Department University of Pittsburgh ======================

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Help for pdb deposition
by qiang liu 14 Feb '11

14 Feb '11

Hi,Dear all, Maybe it's a simple question for you,because I am a beginner in crystallography. Recently I deposited a structure in the pdb and got a reply bellow. "The deposited structure factor file is incomplete. We failed convert the deposited mtz file to cif format. Please send me the correct SF file including h, k, l, F, SigmaF (and/or I and SigmaI)and test flags as an attachment." The mtz file I uploaded is map_coeffs.mtz after refinement.The column lables are listed. type column lable H H H K H L F 2FOFCWT P PH2FOFCWT F 2FOFCWT_no_fill P PH2FOFCWT_no_fill F FOFCWT P PHFOFCWT So how can I get the parameters for deposition in PHENIX? Any suggestions will be appreciated! Thank you very much. Qiang Liu

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difference map
by intekhab alam 12 Feb '11

12 Feb '11

Hi i am trying to calculate a difference map ( ligand-native ) using isomorphous difference map program in phenix. I used the reflection files of ligand and native and phase information of ligand derived data. But the difference map donot fits the ligand, and appears as a circular chunk of density at sigma level 5. I calculated an omit map that clearly showed the presence of my ligand at the specific position. Is there anything wrong in my calculation. What alternate ways are there to improve my difference map. -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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