- phenixbb - phenix-online.org

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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Re: [phenixbb] phenixbb Digest, Vol 52, Issue 12
by Kay Diederichs 11 Mar '10

11 Mar '10

Am 11.03.2010 23:51, schrieb phenixbb-request(a)phenix-online.org: > Message: 4 > Date: Wed, 10 Mar 2010 16:52:35 -0500 > From: Nathaniel Echols<NEchols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] autosol interface bug? selinux conflict? > Message-ID:<6BE2BD93-F43C-4D37-AD91-9F31BCE2C6F1(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii > > On Mar 10, 2010, at 4:37 PM, Kay Diederichs wrote: >> > I wonder >> > - why do Fortran binaries give a SElinux problem, and C++ binaries don't? > Because we bundle the Intel Fortran shared libraries (which are required by SOLVE) with the binary installers. > if you simply link with -static-intel then you don't have to distribute those libraries. HTH, Kay

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Additional residue info in coot
by Brown, Breann 11 Mar '10

11 Mar '10

Hello, I am currently refining a model of a zinc-binding protein and after refinement there is additional positive Fo-Fc density at the zinc site. This is the fourth independent structure of this particular protein solved in my lab so we are confident the metal is in fact zinc. I noticed that after refinement the "residue info" in Coot has two lines for the zinc atom. The first line reads "G/121 ZN/ZN 1.00 44.30" while the second line reads G/121 ZN/ 0.00 0.00. The occupancy for the second line cannot be changed and it only appears after refinement. I carried out the same refinement using a previously solved structure of the same protein and the extra residue info line was not present. My question is where does this extra line in the residue info come from and could the zero occupancy be causing additional Fo-Fc density at the metal site? Thanks, Breann Breann L. Brown Page Laboratory Department of Molecular Pharmacology, Physiology and Biotechnology Brown University Providence, RI 02912

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Re: [phenixbb] autosol interface bug? selinux conflict?
by Kay Diederichs 10 Mar '10

10 Mar '10

Am 11.03.2010 07:00, schrieb phenixbb-request(a)phenix-online.org: > Message: 1 > Date: Wed, 10 Mar 2010 09:28:36 -0500 > From: Nathaniel Echols<NEchols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] autosol interface bug? selinux conflict? > Message-ID:<E0B9BF9F-C96B-4F45-9D02-CC16197AFFF0(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii > > On Mar 9, 2010, at 6:03 PM, Stuart Endo-Streeter wrote: >> After this repetitive route got autosol running, I ran into some kind of >> selinux security warning that blocked autosol and caused it to crash. I >> seem to have fixed that issue by switching temporarily to permissive mode, >> but disabling security to run phenix hardly seems the appropriate solution. >> I didn't manage to catch the autosol error message, I will try to recreate >> it later tonight if needed. > > SELinux breaks the Fortran binaries we distribute. There are two things to try: > > 1. If you installed to /usr/local, try installing to your home directory instead (if this is your computer rather than a shared system). For example: > > computer:~> ./install --prefix=/home/nat/software > > I don't know if this will help or not, but it's worth a try. I wonder - why do Fortran binaries give a SElinux problem, and C++ binaries don't? - does the phenix installer script treat (i.e. label) C++ binaries in any special way which cannot be done for other binaries? If it is known that SElinux is the problem, then this already half of the solution. In general, these problems can easily be found and fixed (on RedHat-derived distros at least) by labelling libraries and binaries in a specific way which is suggested by the output of the SEtroubleshoot- daemon (to be found in /var/log/messages). If that daemon doesn't run, you may have to install it with "yum install setroubleshoot-server". HTH, Kay

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python issues
by Patrick Loll 10 Mar '10

10 Mar '10

Hi, This is really a ccp4-provoked question, but it relates to phaser & cctbx (I think), so I'll try here as well: After an install of ccp4 on a MacBook Pro running Snow Leopard and on a MacPro running Leopard, the command: source /sw*/bin/init.csh (where /sw* is either /sw64 on the machine running 10.6, or /sw on the machine running 10.5) gives the error: ******************************************* Fatal Error: Incomplete libtbx environment! ******************************************* Please re-run the libtbx/configure.py command. If I go to ...ccp4.../src/phaser/phaser-2.1.4/libtbx/ and type python configure.py Then it tells me that the md5 module is deprecated, and that the cool kids use hashlib instead. Does this mean that I need to go to an earlier version of python? Will that mess up other things? Curiously, one machines giving this problem has python 2.5.1, while the other has 2.6. However, I currently have python 2.5.1 running on another machine (albeit with a slightly earlier version of ccp4) and it doesn't give me this problem. Ideas? Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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