- phenixbb - phenix-online.org

Gap between R and Rfree
by Young-Jin Cho 13 Mar '10

13 Mar '10

Hi everyone, I recently got a diffraction data and am trying to refine it. The question is whatever I did the gap between R and Rfree stay far away: .2140/.2982 around 2.5 A resolution. (water added and isotropic(individual_adp) and so on). Although I am redoing with many different approaches, if anyone can give me any comments or suggestions, it would be helpful. Thanks in advance, Young-Jin

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Low resolution structure
by Kendall Nettles 13 Mar '10

13 Mar '10

I have a few questions related to a 3.5 angstrom structure. I have one helix that I am having trouble placing accurately. It does have a cysteine that disulfide bonds with the same residue in a symmetry related molecule. Can I restrain this distance during a rigid body refinement of the helix? How do I do this? What kind of parameters would be appropriate for the disulfide? My second question is whether someone can suggest appropriate distance_ideal, sigma, and slack for hydrogen bond restraints for a helix? Also, I have a 2 angstrom structure of this part of the complex for reference. Thanks! Kendall Nettles

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Re: [phenixbb] phenix gui freezes
by John Berrisford 12 Mar '10

12 Mar '10

Dear All Thanks for the suggestions on how to solve my GUI freezing issues. It looks like it was a communication problem with coot that was causing my problems. Editing App.py as below solved my problem. Adding a preference setting to do this would be useful. Thanks again John Message: 3 Date: Thu, 11 Mar 2010 09:48:29 -0500 From: Nathaniel Echols <NEchols(a)lbl.gov> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] phenix gui freezes Message-ID: <49B2EAFF-6882-4118-8322-E3949BA490DE(a)lbl.gov> Content-Type: text/plain; charset=us-ascii I have one other thought - the GUI listens on a socket for incoming commands from Coot (this isn't used very much at present). Apparently this caused problems on Linux with the old GUI, which also used Python sockets. If something goes wrong here, it could certainly take down the entire program. To fix this, edit the file $PHENIX/phenix/wxGUI2/App.py, and comment out this line (in 1.6): self.start_xmlrpc_server() (if you're new to python, a comment starts with '#'.) I will add a preferences setting to do this. I can also try slowing down the GUI updates while a process is running (using detached processes should also take care of this). -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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naming of refinement runs
by John Berrisford 12 Mar '10

12 Mar '10

Dear All I've been running multiple refinement runs and they are named sequentially. I'm looking for a method to name the refinement runs with the GUI. I understand that I can edit the output file names, but is there anyway to give the refinement runs a title to describe the run as there is in CCP4i? I was thinking along the lines of eg. "Refine_10 - 20 cycles ADP scale 2...." Thanks John -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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Custom ligand - confirming the correct scattering definition
by George Phillips 12 Mar '10

12 Mar '10

Pavel, I am following up on this question of the oxidation state of metals. It is important to deal with this properly to get the most out of the data and to able to show difference maps in papers that make sense. Where are the scattering factors stored (it1992's for example)? One could hack an oxidation state in for the standard numbers to get it right (ugly but effective). Alternatively, maybe the scattering factor tables and element id's could be expanded? Is this all hard coded or are there libraries or tables that are parsed? THanks for any comments, as always. George N. Phillips, Jr., Ph.D. Professor of Biochemistry and of Computer Sciences University of Wisconsin-Madison 433 Babcock Dr. Madison, Wi 53706 Phone/FAX (608) 263-6140 Hi Andy, currently phenix.refine will not make difference between say "Fe" and "Fe+2". So if you see some artifacts at mFo-DFc map around your Fe, that might be explained by not taking "+2" into account. Refining occupancy of Fe would fix the map appearance (most likely), but I would not do that, since it will rather hide the problem than properly address it (and of course it would be misleading too). Regarding "n_gaussian table": it is just a dynamic approximation to the standard scattering factor table (mostly done to optimize runtime; the accuracy is not compromised). For more details see: Grosse-Kunstleve RW, Sauter NK, Adams PD: cctbx news Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3:22-31. Pavel. On 11/25/09 12:37 PM, Andy Torelli wrote: > To the Phenix group: > > I've created a .cif file for a ligand that includes metal atoms. The > metal atoms are defined in the .cif file with their element name, but in > actuality, they should be defined according to their oxidation state so > that the correct scattering parameters are used during refinement. > > In CNS, this meant choosing an "atom type" that would be parsed to > match the correct scattering definition listed in the scatter.lib file. > I see that phenix uses the n_gaussian table for scattering values. > Where can I view this and the other scattering table options? Like CNS, > do I just need to use the name of the element with the correct > oxidation state from the table (e.g. "Fe+2") in my .cif file to ensure > that the correct scattering definition is used during refinement and map > calculation? > > Thanks, > -Andy Torelli > > _______________________________________________ > phenixbb mailing list > phenixbb at phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > Previous message: [phenixbb] Custom ligand - confirming the correct scattering definition Next message: [phenixbb] Confused by the output from Phenix autobuild jobs Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about the phenixbb mailing list George N. Phillips, Jr., Ph.D. Professor of Biochemistry and of Computer Sciences University of Wisconsin-Madison 433 Babcock Dr. Madison, Wi 53706 Phone/FAX (608) 263-6142

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composite omit map command phenix 16
by John Bruning 11 Mar '10

11 Mar '10

Hi, How can I generate a composite omit map from the command line in Phenix16? Thanks, John

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March 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 11 Mar '10

11 Mar '10

Dear Users, The deadline for May/June 2010 Collaborative Crystallography proposals will be *Mar 15, 2010. * ------------------------------------------------------------------------ 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 2010 allocation period, proposals must be submitted by *March 15, 2010.* The deadline for CC proposals for the time period July/August 2010 will be May 15, 2010. Regards, Banumathi Sankaran

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does phenix.refine ignore F-obs, SIGF-obs?
by Scott Classen 11 Mar '10

11 Mar '10

Hi All, I have an mtz file that has: I-obs SIGI-obs F-obs SIGF-obs I want phenix.refine to use F-obs and SIGF-obs, but even though I provide : labels = "F-obs,SIGF-obs" I think phenix.refine is seeing the I-obs,SIGI-obs and recalculating the structure factors from those values instead of using the Fs that I provide in the mtz. Is this the case? Other than stripping the I-obs,SIGI-obs from the input mtz, is there a way to force phenix to use my structure factors? Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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phenix gui freezes
by John Berrisford 11 Mar '10

11 Mar '10

Dear All A little while ago I posted a message about the GUI freezing on linux systems, either run remotely (centos) or locally (ubuntu system). I never received a solution and I'm still having this problem despite upgrading to version 1.6. On my ubuntu system the GUI seems to freeze either when the screen saver comes on (set to turn the screen off) or I switch desktop - although not everytime I do this. The freezing GUI means that I have to force quit phenix after every refinement run (I haven't tried other tasks) and that the freeR is not reported to the GUI (not a major problem). Thankfully in version 1.6 the configuration and results for each refinement run are recorded and I can retrieve this information by loading a job through job history - a big improvement over version 1.5. Anyone else having this problem and does anyone know a solution? Thanks John -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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Re: [phenixbb] does phenix.refine ignore F-obs, SIGF-obs?
by Scott Classen 11 Mar '10

11 Mar '10

Here are some excerpts from the phenix.refine log file: Resolution range: 44.4024 1.8604 Completeness in resolution range: 0.995991 Completeness with d_max=infinity: 0.995862 Number of F-obs in resolution range: 92411 Number of F-obs <= 0: 3322 Refinement resolution range: d_max = 44.4024 d_min = 1.8604 Fobs statistics after all cutoffs applied: Miller array info: None Observation type: xray.amplitude Type of data: double, size=89089 Type of sigmas: double, size=89089 Number of Miller indices: 89089 Anomalous flag: False Systematic absences: 0 Centric reflections: 11672 Resolution range: 44.4024 1.8604 Completeness in resolution range: 0.960187 Completeness with d_max=infinity: 0.960063 This implies to me that phenix.refine is throwing out my very weak reflections. It appears that completeness goes from 99.6% to 96.0% Then further down in the log file I see: ============================== Outliers rejection ============================= Distribution of F-obs values before outliers rejection: 0.126 - 28.714 : 65519 28.714 - 57.302 : 13850 57.302 - 85.890 : 5625 85.890 - 114.478 : 2515 114.478 - 143.066 : 991 143.066 - 171.654 : 393 171.654 - 200.242 : 128 200.242 - 228.830 : 49 228.830 - 257.418 : 12 257.418 - 286.006 : 7 basic_wilson_outliers = 0 extreme_wilson_outliers = 0 beamstop_shadow_outliers = 0 model_based_outliers = 1 total = 1 Distribution of F-obs values after outliers rejection: 0.126 - 28.714 : 65519 28.714 - 57.302 : 13850 57.302 - 85.890 : 5624 85.890 - 114.478 : 2515 114.478 - 143.066 : 991 143.066 - 171.654 : 393 171.654 - 200.242 : 128 200.242 - 228.830 : 49 228.830 - 257.418 : 12 257.418 - 286.006 : 7 which makes it look like nothing is being rejected? So what is it? in the header of the resulting pdb file: REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.860 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.402 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.03 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.02 REMARK 3 NUMBER OF REFLECTIONS : 89088 which implies that indeed some reflections are being rejected. My hunch is that if F-obs = SIGF-obs then the reflection is rejected. Thanks, Scott

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