- phenixbb - phenix-online.org

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 12 Mar '10

12 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 12 Mar '10

12 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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Re: [phenixbb] autosol interface bug? selinux conflict?
by Nathaniel Echols 10 Mar '10

10 Mar '10

On Mar 9, 2010, at 6:03 PM, Stuart Endo-Streeter wrote: > Problem is, column labels are selected. "i_obs sigma" is showing in the > label field for each dataset. Clicking on the field to try to re-select > makes no difference, I still get the same error message. If I load just a > single anomalous dataset in addition to the native dataset, usually autosol > will run, sometimes not. It does not matter which anomalous dataset I am > using. If I load the native and only one of the anomalous datasets it > usually works. If I then repeat the process of adding a single anomalous > dataset, running autosol, aborting the run, then adding the next dataset, > eventually I can add all the datasets and start autosol. I'm not sure what to suggest, because I can't reproduce this (with 1.6 or the latest code), nor could I find anything in the code that indicates how it happens. Could you please send me a screenshot of the GUI before you click Run? > 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. 2. Install from source. This will take several hours, so if you have multiple cores we recommend adding the flag "--nproc=8" (or whatever) when you run the install script. If you have access to the Intel Fortran compiler we recommend installing and configuring that (I think the build script will switch to using it automatically), since g77/gfortran produce binaries that are *much* slower. This problem should go away in a few months when we purge the last FORTRAN code from PHENIX. -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 NEchols(a)lbl.gov

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autosol interface bug? selinux conflict?
by Stuart Endo-Streeter 09 Mar '10

09 Mar '10

Dear board... I am trying to run autosol with a native dataset and a mad experiment to extend the phases. Unfortunately I cannot even begin the actual process (without some weird convolutions) because phenix keeps giving the following message: "You must select a column label to use in each reflection file. If no labels are shown in the drop-down menu, it may not be a valid format." Problem is, column labels are selected. "i_obs sigma" is showing in the label field for each dataset. Clicking on the field to try to re-select makes no difference, I still get the same error message. If I load just a single anomalous dataset in addition to the native dataset, usually autosol will run, sometimes not. It does not matter which anomalous dataset I am using. If I load the native and only one of the anomalous datasets it usually works. If I then repeat the process of adding a single anomalous dataset, running autosol, aborting the run, then adding the next dataset, eventually I can add all the datasets and start autosol. 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. My system is CentOS 5.4, gui is KDE, phenix is v1.6, installed just yesterday. Any suggestions/clues would be appreciated. Stuart Endo-Streeter ________________________________ Stuart Endo-Streeter, Ph.D Dept. Computer Science Duke University Medical Center 3245 French Family Sciences Building 919-660-4018 stuart.endostreeter(a)duke.edu

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anisotropic refinement water hydrogens and gui
by Christian Roth 09 Mar '10

09 Mar '10

Dear all, I did an anisotropic refinement with the gui for a 1.6 Ang. structure I think this is quite O.K. as the R-values seems to be reasonable(14/18.8). But for comparison I want exclude waters and hydrogens explicitly from the anistropic refinement. One could do this in the command line mode via adp.individual.anisotropic ="not water and not element H. I started from the gui and modified the .eff directly by icnluding: adp { individual { isotropic = None anisotropic = "not water and not element H" In the output pdb all waters have an anisou flag. So I assume phenix refined them anisotropically. How do I have to modify the .eff file to exclude the waters from the anisotropic refinement. I would like to use the gui, because you get this nice summary output with all statistics. Phenix started optionally anisotropic refinement at 1.7 Ang. As far as I understand one should keep in mind that the data to parameter ration should have certain value of app. 3 or 4. But restraints as paramters are not as solid as experimental data. Is this 1.7 Ang. borderline a rule of thumb, is there a strict rule at which point I could refine anisotropic, or maybe mixed isotropic anisotropic. Best regards Christian

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phenix.refine and multi-metals centers
by Carlos Frazao 09 Mar '10

09 Mar '10

Hi I have a doubt on the refinement of e doubled metal center. I know that: 1) one may fix the metals to their actual positions by using e.g. refine.sites.individual="not element Fe" 2) one may use "phenix.metal_coordination my.pdb" to obtain a dictionary for the actual metals coordinations but how does phenix.refine handels metal-to-metal interactions? How should one set the refinement of a metallo protein with a two metals centre, in order not to bias the final result (metal to metal distances) ? Thanks a lot, Carlos -- ************************************** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, Portugal Phone: (351)-214469666 FAX: (351)-214433644 e-mail: frazao(a)itqb.unl.pt www.itqb.unl.pt

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molprobity todo list and coot integration in linux
by hari jayaram 09 Mar '10

09 Mar '10

Hi, Is a difference in the way the GUI molprobity TODO list is displayed between linux and Mac OSX . I am running 1.6.289 on both ...and have coot with scheme and python scripting installed, On mac OSX , phenix starts up coot with the molecule and maps loaded after a phenix.validate and a TO-DO list in a separate GUI window In Linux these separate To-do list windows dont seem to open . ..I have looked everywhere and the dont seem burried behind something else, Is there some setting I need to toggle to have these popup , sortable todo lists for molprobity assisted rebuilding on Linux systems? Thanks for your help Hari

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Autosol + MR
by Manoj saxena 07 Mar '10

07 Mar '10

Hi, I have partial solution from MR on a crystal with dimensions 52.729 60.364 142.908 90.00 90.00 90.00 P 21 21 21. I have SAD data from another crystal with dimension 53.860 61.470 142.492 90.00 90.00 90.00 P 21 21 21. My question is can I treat both as isomorphous and combine data from both of them and use my MR as model with Autosol. What is the maximum difference in unit cell dimensions allowed to consider two unit cell isomorphous? If you can point to some references/examples that will be highly appreciated. Thanks a lot. Marusa

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phenix.reduce segmentation fault with -trim option on Snow leopard Mac OSX
by hari jayaram 05 Mar '10

05 Mar '10

Hi I am running the phenix.reduce with the -trim option and getting a segmentation fault with phenix version 1.6.289 I will remove the molprobity introduced hydrogens using pdbtools ..but thought I will write in with this Thanks Hari $ phenix.reduce s3-3_2.1_refmac0-coot-15_refmac0FH.pdb -trim > s3-3_2.1_refmac0-coot-15_refmac0FnoH.pdb reduce: version 3.15 11/6/2009, Copyright 1997-2009, J. Michael Word Processing file: "s3-3_2.1_refmac0-coot-15_refmac0FH.pdb" Segmentation fault

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coot integration require coot with python?
by hari jayaram 04 Mar '10

04 Mar '10

Hi Is it likely that the phenix-coot integration with the new GUI requires a python infused coot ?. Although I have set the coot path correctly nothing happens after coot launches . I am using the ccp4 6.1.3 coot 0.6 (revision 2540) [with guile 1.8.3 embedded] and phenix 1.6.289 on OSX snow leopard 10.6.2. I know the ccp4 coot does not come with python scripting support ...the pymol integration seems fine , but coot just sits there with an empty window after a phenix.validate run. Any ideas on how to have them talking to each other? Thanks Hari

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autosol and NCS
by hli＠uci.edu 04 Mar '10

04 Mar '10

I have solved a structure by MR with Phaser. There are 4 copies of molecules per ASU. Parts of the search model are not agreeable with the new structure leading to messy density in some regions. Now a set of SAD data has been collected. I want to run Autosol (MRSAD) to combine the SAD and model phases, doing density modification including the NCS. Can I run simple_ncs_from_pdb to get the NCS operators from the MR solution pdb file and use them for Autosol? Thanks for help. Huiying UC Irvine

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Phaser phasing power statistics
by Daqi Tu 03 Mar '10

03 Mar '10

Hi, I was trying to find phasing power statistics from phenix.autosol log file but couldn't. My structure was phased by Phaser SAD module in phenix.autosol, all I could find was figure of merit. I then ran Phaser SAD within CCP4 and still could not find phasing power statistics from its log. Does anyone know if Phaser SAD generates phasing power statistics in its log file at all? Thanks. Daqi Tu Postdoc Eck lab Harvard medical school

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SAD + Xray = ???
by J. Fleming 02 Mar '10

02 Mar '10

Hi, I have a set of Se-Met SAD data, high resolution x-ray data, and a protein sequence. Is there a way to combine these data sets in Phenix and carry out an autobuild? I saw a section in the manual about MRSAD but that requires a starting model. I've used the SAD data alone to generate a model but I'd like to use both data sets together. Thanks for your thoughts, -Jon

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ICCBM13 - Call for abstracts now open!
by Valerie Pye 02 Mar '10

02 Mar '10

Apologies for this being off topic - but may be of general interest: * * * * *13th International Conference on the Crystallisation of Biological Macromolecules* Trinity College Dublin, Ireland 12th – 16th September 2010 *Crystallization Workshop* – 9th – 12th September 2010 Call for Abstracts Now Open <http://www.iccbm13.ie/abstracts.html> The *13th International Conference on the Crystallisation of Biological Macromolecules* (*ICCBM13 <http://www.iccbm13.ie/>*) is the meeting of choice to learn about the latest research and developments in biomacromolecular crystallogenesis for structure-function-rational design applications. At ICCBM13 leading academic and pharmaceutical scientists will report on challenging systems to include macromolecular complexes and membrane proteins with an emphasis on novel practical as well as mechanistic aspects of crystallogenesis. To cater to the needs of the individual wanting to learn how to grow crystals or to acquire new crystallisation skills, the Conference is preceded by a *Workshop <http://www.iccbm13.ie/workshop.html>* devoted to hands-on instruction on select aspects of macromolecule production and crystal growth. The Conference will be held at *Trinity College Dublin <http://www.tcd.ie/>, Ireland* from the 12th to the 16th September 2010. Convenient and affordable housing is available on and around Trinity College. The campus is situated in the heart of Ireland’s capital city and is surrounded by a diversity of restaurants, pubs, theatres and other points of interests. *Scholarships <http://www.iccbm13.ie/scholarships.html>* are available to Graduate Students and Postdoctoral Fellows. Additional information is available at *www.iccbm13.ie* *ICCBM13 Congress Secretariat* T: + 353 (0) 1 400 3626 F: + 353 (0) 1 400 3692 E: info(a)iccbm13.ie W: www.iccbm13.ie *C/O Keynote PCO* Suite 26, Anglesea House, Blackrock Co. Dublin, Ireland www.keynotepco.ie

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twin refinement
by subhash bihani 02 Mar '10

02 Mar '10

Hi i am refining a protein strucutre with space group P61. Intesity statistics doesnot suggest any twining but refmac and phenix xtriage suggest a twin operator with fraction 0.48. when refined with this twin operator R factors come dowm by 3-5% and also map looks much better. but upon closer inspceion it seems that maps are heavily biased toward the model in both refmac and phenix ( I have mutated one lysine to his and it changed the map to cover his). my question is why twin refinement maps are biased and what are the ways to overcome this. my second question is how to decide whether to use twin refinement or not. is it depends on R factor statistics or we have to check some other parameters. thanks in advance subhash bihani scientific officer Bhabha Atomic Research Centre Trombay-400085 Mumbai(M.S.) India Ph. +912594688 (o) +919322191020 -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

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NCS restraints
by Mirek Cygler 28 Feb '10

28 Feb '10

Hi, I have NCS symmetry in my crystal and wouldlike to use it during the refinement. What is the strength of the restraints for the backbone, for the sidechains? How can I control these restraints? Thanks, Mirek

3 2

Clarification on ADPs in PDB files for TLS refinement ?
by Phil Jeffrey 27 Feb '10

27 Feb '10

Hi, Having a discussion with a colleague yesterday on differences in Phenix and Refmac representations of TLS B-factors in the PDB file I came across two different definitions for what the PDB ANISOU U's correspond to as written by Phenix: 1. From necat.chem.cornell.edu/workshops/.../WK04_PavelAfonine.pdf on p.20 U(TOTAL)= U(ATOM) + U(TLS) + U(CRYST) and only U(atom) + U(tls) is stored in the PDB ANISOU card. 2. From http://proteincrystallography.org/ccp4bb/message8948.html "Utotal = Utls + Ulocal + Ucryst. So, the ANISOU records always contain Utotal and ATOM records contain isotropic equivalent of Utotal" Which is not the same thing. I suspect it's #1. Am I right ? I would think that U(cryst) is potentially a non-zero contribution to atomic ANISOU values but is actually applied before the TLS/Anisotropic B-factors are refined. As a tie-breaker between #1 and #2 the program documentation suggest that it is just U(tls)+U(atom) but the paragraph that nominally explains it is not short of of inconsistencies, referring to the ANISOU record as having the "the total B-factor (B_tls + B_individual)" whereas they're not only not B's (they are U's) but it's also not the *total* U or B by its own definitions. IMHO it would warrant a rewrite for clarity since B and U are used interchangeably and "total" has variable usage. Phil Jeffrey Princeton

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Re: [phenixbb] Map after refinement
by Xuewu Zhang 27 Feb '10

27 Feb '10

To Paul, No, I used the mtz format map file in coot. TO Pavel, I will send you the files tomorrow. The command I used is the simplest one: phenix.refine input.pdb input.mtz. By the way, the same thing happened to one of my colleagues here a while ago. She solved the problem by updating to the then new 1.5 version. Thanks you guys for the quick replies. Xuewu Zhang UT Southwestern Medical Center On Fri, Feb 26, 2010 at 4:29 PM, <phenixbb-request(a)phenix-online.org> wrote: > 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. Int'l Workshop on Macromolecular Crystallography - South > America (Alejandro Buschiazzo) > 2. Re: Gap between R and Rfree (Felix Frolow) > 3. Re: Map after refinement (Xuewu Zhang) > 4. Re: Map after refinement (Paul Adams) > 5. Re: Map after refinement (Pavel Afonine) > 6. weaker density in maps (David Garboczi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 26 Feb 2010 18:17:06 -0200 > From: Alejandro Buschiazzo <alebus(a)pasteur.edu.uy> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Int'l Workshop on Macromolecular Crystallography - > South America > Message-ID: <4B882C42.9080701(a)pasteur.edu.uy> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Dear colleagues, > > just a reminder, we're close to the deadline for applications. Details > below. > > Thank you! > > > ----------------------------------------------------------------------------------------------------------------------- > > *International Workshop ?Macromolecular Crystallography : Introduction > and Applications"* > > *April 26 - May 7, 2010* > > *Institut Pasteur de Montevideo* > > *Uruguay* > > The principal aim of this course, is to give intense hands-on training > in all main aspects of macromolecular 3D structure determination by X > ray diffraction. > > The course will include lectures delivered by a number of > international experts in the discipline, linked to hands-on > experimental work and demonstrations. > > Special emphasis will be given to : > > * Experiment design : manual and robotic crystallogenesis of > macromolecules, X ray diffraction of single crystals, data collection > * Diffraction data processing > * Model refinement and structural analysis > > > *ACTIVITY INTENDED FOR* > > * Graduate Students (MSc and PhD) > * Postdocs > * Young Research Scientists > > > *APPLICATION REQUIREMENTS* > > Candidates should send the following information : > > 1. -Short CV (including age, current position, scientific interests, > publications) > 2. -Letter of motivation (the applicant should stress how > Macromolecular Crystallography is included in her/his ongoing > scientific project) > 3. -Reference letter from the apllicant's supervisor > > > *SCHOLARSHIPS* > > Inscription fees are fully covered for all accepted students. > Applicants from abroad with no financial support, are welcome to apply > for a lodging and per diem expenses scholarship. This should be > inlcuded as a separate document at the time of application. A limited > number of traveling aids will be available: arguments backing this > request should be duly explained, to be evaluated on a case by case > basis. > > *APPLICATION DEADLINE* > > All applications should be received until March 7 2010. They should be > sent as a single pdf document to : crystallography(a)pasteur.edu.uy > > *ORGANIZERS* > > Dr. Alejandro Buschiazzo > Unidad de Cristalograf?a de Prote?nas > Institut Pasteur de Montevideo > > Dr. Pedro Alzari > Departamento de Biolog?a Estructural y Qu?mica > Institut Pasteur de Paris > > Dr. William Shepard > Proxima 2 > Synchrotron Soleil > > For further information, please E-mail to crystallography(a)pasteur.edu.uy > > The official language of the course will be english. > > Detailed information is available at: > http://www.pasteur.edu.uy/mxcourse Please check for regular updates of > the program. > > *FUNDING* > > RIIP, AMSUD/PASTEUR, IP MONTEVIDEO (URUGUAY INNOVA), CeBEM > > This International Workshop is part of the activities of the Center of > Structural Biology of Mercosur (Centro de Biolog?a Estructural del > Mercosur - CeBEM) > > > > > -- > Alejandro Buschiazzo, PhD > Research Scientist > Laboratory of Protein Crystallography > Pasteur Institute of Montevideo > Mataojo 2020 > Montevideo 11400 > URUGUAY > > Phone: +5982 5220910 int. 120 > Fax: +5982 5224185 > > > > ------------------------------ > > Message: 2 > Date: Fri, 26 Feb 2010 22:18:33 +0200 > From: Felix Frolow <mbfrolow(a)post.tau.ac.il> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Gap between R and Rfree > Message-ID: <F52C4FE8-AE34-4C23-B74E-A923995E5831(a)post.tau.ac.il> > Content-Type: text/plain; charset=us-ascii > > Yea Phil, You have got them > I was accused several years ago for over-fitting Rfree !!!!!!! > The bad thing is that to publish you have to avoid arguing with these > post-crystallography era referees. > Today they ask meaningless question " I am novice to crystallography, teach > me how to minimize Rfree" > Tomorrow they referee you papers and make meaningless remarks about gap > between R and Rfree > " Your R factor is 17% and Rfree is 24%, it rase question" > geeeeek!!!!!! what question????? > Dr Felix Frolow > Professor of Structural Biology and Biotechnology > Department of Molecular Microbiology > and Biotechnology > Tel Aviv University 69978, Israel > > Acta Crystallographica D, co-editor > > e-mail: mbfrolow(a)post.tau.ac.il > Tel: ++972 3640 8723 > Fax: ++972 3640 9407 > Cellular: ++972 547 459 608 > > On Feb 26, 2010, at 11:30 , Phil Evans wrote: > > > > > I do worry a bit about the fetishisation of R-factors, to the point where > I get the impression that some people think that the object of refinement is > minimisation of Rfree. The aim is to produce the "best" model consistent > with the data, and the most important tool is looking at the maps on the > graphics, in conjunction with validation tools analysing consistency with > what we know about stereochemistry (Ramachandran, rotamers, bumps etc). Also > is your model consistent with your initial experimental phased map, if > available? The Rfree is a useful guide, but no more than that. > > > > My (admittedly superficial) experience of changing weights, freeR > selection, resolution limits, NCS, etc in refinement is that often you can > spend some time doing this, maybe improve the R-factors a bit, but end up > with a model which is indistinguishable from the previous model when > superimposed on it. > > > > I'm fed up with referees telling me my structure must be wrong because > the Rfree is "too high" (and I haven't followed their particular pet > protocol), when I know that it is essentially correct, and as good as I can > make it. > > > > Phil > > > > > > On 26 Feb 2010, at 01:49, Pavel Afonine wrote: > > > >> Hi Simon, > >> > >> the next available PHENIX nightly build will have this command: > >> > >> phenix.r_factor_statistics > >> > >> This will output a plain text histograms for Rwork, Rfree and > Rfree-Rwork. For example: > >> > >> *** > >> phenix.r_factor_statistics 2.5 left_offset=0.2 right_offset=0.2 n_bins=5 > >> Command used: > >> > >> phenix.r_factor_statistics 2.500 left_offset=0.200 right_offset=0.200 > n_bins=5 > >> > >> > >> Histogram of Rwork for models in PDB at resolution 2.30-2.70 A: > >> 0.115 - 0.168 : 149 > >> 0.168 - 0.220 : 2998 > >> 0.220 - 0.273 : 1879 > >> 0.273 - 0.325 : 67 > >> 0.325 - 0.378 : 2 > >> Histogram of Rfree for models in PDB at resolution 2.30-2.70 A: > >> 0.146 - 0.210 : 116 > >> 0.210 - 0.274 : 3288 > >> 0.274 - 0.337 : 1664 > >> 0.337 - 0.401 : 26 > >> 0.401 - 0.465 : 1 > >> Histogram of Rfree-Rwork for all model in PDB at resolution 2.30-2.70 A: > >> 0.001 - 0.021 : 233 > >> 0.021 - 0.041 : 1412 > >> 0.041 - 0.060 : 2180 > >> 0.060 - 0.080 : 1045 > >> 0.080 - 0.100 : 225 > >> Number of structures considered: 5095 > >> *** > >> > >> and running it without arguments will take all structures. > >> > >> Pavel. > >> > >> > >> > >> On 2/25/10 2:01 PM, Simon Kolstoe wrote: > >>> oh yes please Pavel (command line polygon/statistics overview) - could > the output be a pdf or ps rather than just starting up the GUI? > >>> > >>> Simon > >>> > >>> > >>> > >>> On 25 Feb 2010, at 19:39, Pavel Afonine wrote: > >>> > >>>> Hi Francis, > >>>> > >>>> in PHENIX GUI: "Validation" -> "PDB Statistics Overview" > >>>> > >>>> or: > >>>> > >>>> in PHENIX GUI: "Validation" -> "POLYGON" > >>>> > >>>> The underlying idea is published here: > >>>> > >>>> Crystallographic model quality at a glance. L. Urzhumtseva, P. V. > Afonine, P. D. Adams, A. Urzhumtsev Acta Cryst. D65, 297-300 (2009) > >>>> > >>>> I can add a command line version if anyone is interested. > >>>> > >>>> Pavel. > >>>> > >>>> > >>>> > >>>> On 2/25/10 9:45 AM, Francis E Reyes wrote: > >>>>> Pavel > >>>>> > >>>>> What phenix utility produces such information? > >>>>> Thx > >>>>> > >>>>> FR > >>>>> > >>>>> On Feb 25, 2010, at 10:43 AM, Pavel Afonine <PAfonine(a)lbl.gov> > wrote: > >>>>> > >>>>>> Hi Young-Jin, > >>>>>> > >>>>>> the distribution of R-factors for all structures in PDB refined at > resolutions between 2.4 and 2.6 A is following: > >>>>>> > >>>>>> Histogram of Rwork for all model in PDB at resolution 2.40-2.60: > >>>>>> 0.115 - 0.141 : 5 > >>>>>> 0.141 - 0.168 : 69 > >>>>>> 0.168 - 0.194 : 414 > >>>>>> 0.194 - 0.220 : 955 <<<<< your structure > >>>>>> 0.220 - 0.246 : 695 > >>>>>> 0.246 - 0.273 : 153 > >>>>>> 0.273 - 0.299 : 25 > >>>>>> 0.299 - 0.325 : 5 > >>>>>> 0.325 - 0.352 : 0 > >>>>>> 0.352 - 0.378 : 1 > >>>>>> Histogram of Rfree for all model in PDB at resolution 2.40-2.60: > >>>>>> 0.146 - 0.178 : 3 > >>>>>> 0.178 - 0.210 : 41 > >>>>>> 0.210 - 0.242 : 404 > >>>>>> 0.242 - 0.274 : 1104 > >>>>>> 0.274 - 0.305 : 653 <<<<< your structure > >>>>>> 0.305 - 0.337 : 108 > >>>>>> 0.337 - 0.369 : 8 > >>>>>> 0.369 - 0.401 : 0 > >>>>>> 0.401 - 0.433 : 0 > >>>>>> 0.433 - 0.465 : 1 > >>>>>> Histogram of Rfree-Rwork for all model in PDB at resolution > 2.40-2.60: > >>>>>> 0.002 - 0.012 : 28 > >>>>>> 0.012 - 0.022 : 83 > >>>>>> 0.022 - 0.031 : 232 > >>>>>> 0.031 - 0.041 : 430 > >>>>>> 0.041 - 0.051 : 458 > >>>>>> 0.051 - 0.061 : 493 > >>>>>> 0.061 - 0.071 : 298 > >>>>>> 0.071 - 0.080 : 186 > >>>>>> 0.080 - 0.090 : 85 <<<<< your structure > >>>>>> 0.090 - 0.100 : 29 > >>>>>> > >>>>>> which I interpret as your Rwork is most likely good as well as > Rfree, but the gap Rfree-Rwork is too large meaning possible overfitting. > >>>>>> > >>>>>> A few tips: > >>>>>> - if you have NCS - use it in refinement; > >>>>>> - optimize refinement target weights: a) automatically: > "optimize_wxc=true optimize_wxu=true", or b) manually using wxc_scale and > wxu_scale parameters; > >>>>>> - make sure you use the latest PHENIX version. > >>>>>> > >>>>>> Let me now if you have any questions. > >>>>>> > >>>>>> Pavel. > >>>>>> > >>>>>> > >>>>>> On 2/25/10 9:17 AM, Young-Jin Cho wrote: > >>>>>>> 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 > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> phenixbb mailing list > >>>>>>> phenixbb(a)phenix-online.org > >>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb > >>>>>>> > >>>>>> _______________________________________________ > >>>>>> phenixbb mailing list > >>>>>> phenixbb(a)phenix-online.org > >>>>>> http://phenix-online.org/mailman/listinfo/phenixbb > >>>>> _______________________________________________ > >>>>> phenixbb mailing list > >>>>> phenixbb(a)phenix-online.org > >>>>> http://phenix-online.org/mailman/listinfo/phenixbb > >>>> _______________________________________________ > >>>> phenixbb mailing list > >>>> phenixbb(a)phenix-online.org > >>>> http://phenix-online.org/mailman/listinfo/phenixbb > >>> > >>> _______________________________________________ > >>> phenixbb mailing list > >>> phenixbb(a)phenix-online.org > >>> http://phenix-online.org/mailman/listinfo/phenixbb > >> _______________________________________________ > >> phenixbb mailing list > >> phenixbb(a)phenix-online.org > >> http://phenix-online.org/mailman/listinfo/phenixbb > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > > > ------------------------------ > > Message: 3 > Date: Fri, 26 Feb 2010 14:31:26 -0600 > From: Xuewu Zhang <xuewu.zhang(a)gmail.com> > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Map after refinement > Message-ID: > <926abad51002261231g71b81d30o48b7ab63f41ba820(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Phenix developers/gurus, > I got a SAD structure, the experimental map (overall_best_denmod..mtz) from > Autosol looks great. I then built the model and used phenix.refine to > refine > the model using the "exptl_fobs....mtz", which worked well as shown by the > lowered Rfree. However, the map from the refinement makes no sense at all, > totally featureless. Using the same refined model and mtz, > phenix.model_vs_data did make the right map. I have tried both phenix 1.5 > and 1.6. Any clue? > Thanks, > Xuewu Zhang > UT Southwestern Medical Center >

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Re: [phenixbb] Map after refinement
by Xuewu Zhang 26 Feb '10

26 Feb '10

Hi Phenix developers/gurus, I got a SAD structure, the experimental map (overall_best_denmod..mtz) from Autosol looks great. I then built the model and used phenix.refine to refine the model using the "exptl_fobs....mtz", which worked well as shown by the lowered Rfree. However, the map from the refinement makes no sense at all, totally featureless. Using the same refined model and mtz, phenix.model_vs_data did make the right map. I have tried both phenix 1.5 and 1.6. Any clue? Thanks, Xuewu Zhang UT Southwestern Medical Center

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Int'l Workshop on Macromolecular Crystallography - South America
by Alejandro Buschiazzo 26 Feb '10

26 Feb '10

Dear colleagues, just a reminder, we're close to the deadline for applications. Details below. Thank you! ----------------------------------------------------------------------------------------------------------------------- *International Workshop “Macromolecular Crystallography : Introduction and Applications"* *April 26 - May 7, 2010* *Institut Pasteur de Montevideo* *Uruguay* The principal aim of this course, is to give intense hands-on training in all main aspects of macromolecular 3D structure determination by X ray diffraction. The course will include lectures delivered by a number of international experts in the discipline, linked to hands-on experimental work and demonstrations. Special emphasis will be given to : * Experiment design : manual and robotic crystallogenesis of macromolecules, X ray diffraction of single crystals, data collection * Diffraction data processing * Model refinement and structural analysis *ACTIVITY INTENDED FOR* * Graduate Students (MSc and PhD) * Postdocs * Young Research Scientists *APPLICATION REQUIREMENTS* Candidates should send the following information : 1. -Short CV (including age, current position, scientific interests, publications) 2. -Letter of motivation (the applicant should stress how Macromolecular Crystallography is included in her/his ongoing scientific project) 3. -Reference letter from the apllicant's supervisor *SCHOLARSHIPS* Inscription fees are fully covered for all accepted students. Applicants from abroad with no financial support, are welcome to apply for a lodging and per diem expenses scholarship. This should be inlcuded as a separate document at the time of application. A limited number of traveling aids will be available: arguments backing this request should be duly explained, to be evaluated on a case by case basis. *APPLICATION DEADLINE* All applications should be received until March 7 2010. They should be sent as a single pdf document to : crystallography(a)pasteur.edu.uy *ORGANIZERS* Dr. Alejandro Buschiazzo Unidad de Cristalografía de Proteínas Institut Pasteur de Montevideo Dr. Pedro Alzari Departamento de Biología Estructural y Química Institut Pasteur de Paris Dr. William Shepard Proxima 2 Synchrotron Soleil For further information, please E-mail to crystallography(a)pasteur.edu.uy The official language of the course will be english. Detailed information is available at: http://www.pasteur.edu.uy/mxcourse Please check for regular updates of the program. *FUNDING* RIIP, AMSUD/PASTEUR, IP MONTEVIDEO (URUGUAY INNOVA), CeBEM This International Workshop is part of the activities of the Center of Structural Biology of Mercosur (Centro de Biología Estructural del Mercosur - CeBEM) -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185

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Which is the website to check if we have a good r free value?
by Sam Stampfer 26 Feb '10

26 Feb '10

Hi, Does anyone know which website is the one where you can compare your pdb file to others of similar resolution to see whether your file has a good r free value for its resolution? Specifically, I have a 2.8 Angstrom resolution structure with an rfree of 24. Thanks, -Sam

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Re: [phenixbb] refinement of N-glycosylation
by Nathaniel Echols 25 Feb '10

25 Feb '10

On Feb 25, 2010, at 1:35 PM, Georg Mlynek wrote: > 2) From the command line everything is perfect now, but as I also want to know how to do this with the gui (version 1.6-289), I added the files BMA.cif file and the apply_cif_link.params together with my coordinates and the mtz in the Input files. But I get following error message: > > <image001.png> > > Is this a Bug? Probably. Could you please send me (not the list) the final configuration files created by phenix.refine from both the command-line and the GUI? thanks, Nat ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 NEchols(a)lbl.gov

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Re: [phenixbb] refinement of N-glycosylation
by Ling Qin 25 Feb '10

25 Feb '10

Dear Georg, Maybe you need to use quotation marks? I also have n-glycosylation and I in my .eff file there is: } apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = "chain A and resname NAG and resid XXX" residue_selection_2 = "chain A and resname ASN and resid XXX" } Hope this is useful. Please correct me if I am wrong. Ling On Wed, Feb 24, 2010 at 1:13 PM, Georg Mlynek <georg.mlynek(a)univie.ac.at>wrote: > Dear All, > > > > I´m quite new to crystallography and I´m refining a structure with > ASN-NAG-NAG-BMA attached and already got help from Blaine who told me how to > do it, but I´m making a small mistake somewhere and can´t figure out what > I´m doing wrong. Must be just one paranthesis or so, I guess. > > In command line just for testing I put: > > phenix.refine refine_data.mtz refine_1-coot-1FrenumberedGlu.pdb > cif_link.params BMA.cif strategy=individual_sites+individual_adp > main.number_of_macro_cycles=2 --overwrite > > > > where I put in cif_link.params as suggested in the mailing list > http://www.phenix-online.org/pipermail/phenixbb/2009-November/002837.htmlwi… and without paranthesis at the beginning > > > > } > > apply_cif_link { > > data_link = NAG-ASN > > residue_selection_1 = chain A and resname NAG and resid 500 > > residue_selection_2 = chain A and resname ASN and resid 297 > > } > > apply_cif_link { > > data_link = BETA1-4 > > residue_selection_1 = chain A and resname NAG and resid 500 > > residue_selection_2 = chain A and resname NAG and resid 501 > > } > > apply_cif_link { > > data_link = BETA1-4 > > residue_selection_1 = chain A and resname NAG and resid 501 > > residue_selection_2 = chain A and resname BMA and resid 502 > > } > > apply_cif_link { > > data_link = ALPHA1-3 > > residue_selection_1 = chain A and resname BMA and resid 502 > > residue_selection_2 = chain A and resname MAN and resid 503 > > > > and suggested by Blaine with and without paranthesis at the beginning > > > > refinement.pdb_interpretation.apply_cif_link { > > data_link = NAG-ASN > > residue_selection_1 = chain A and resname NAG and resid 500 > > residue_selection_2 = chain A and resname ASN and resid 297 > > } > > refinement.pdb_interpretation.apply_cif_link { > > data_link = BETA1-4 > > residue_selection_1 = chain A and resname NAG and resid 500 > > residue_selection_2 = chain A and resname NAG and resid 501 > > } > > refinement.pdb_interpretation.apply_cif_link { > > data_link = BETA1-4 > > residue_selection_1 = chain A and resname NAG and resid 501 > > residue_selection_2 = chain A and resname BMA and resid 502 > > } > > refinement.pdb_interpretation.apply_cif_link { > > data_link = ALPHA1-3 > > residue_selection_1 = chain A and resname BMA and resid 502 > > residue_selection_2 = chain A and resname MAN and resid 503 > > > > I see in the .geo file that the residues are not bonded, and also in the > .eff file that these lines are not added there, which should be done I > guess, I put the info also direct into the .def file but I get the same > problem? > > > > By the way it shouldn´t matter which name I give to this file as long as > the extension is correct? > > > > Thank you very much and all the best, Georg. > > > > > > > > -----Ursprüngliche Nachricht----- > Von: phenixbb-bounces(a)phenix-online.org [mailto: > phenixbb-bounces(a)phenix-online.org] Im Auftrag von Ursula Schulze-Gahmen > Gesendet: Dienstag, 23. Februar 2010 19:20 > An: phenixbb(a)phenix-online.org > Betreff: [phenixbb] weights optimization, add hydrogens > > > > I am refining a 2.0 A structure in Phenix using mostly the graphical > > interface. The maps are very good and the R factors are low > > (0.208/0.173). But the geometry is not so great with bond deviations of > > 0.208 and Angle deviations of 1.85. What is the best thing to do to try > > to improve the geometry. Should I try to optimize the weights? > > > > The other question is about adding hydrogens to the model. I did add > > them in a previous refinement cycle. After rebuilding the model in coot, > > most of the model still has the hydrogens in the input file for the next > > refinement cycle, but some residues and waters don't have hydrogens. > > When I tried to add hydrogens again to the model, I got an error message > > about atoms being to close. Does Phenix know where to add hydrogens if > > the input model has already hydroegns on many residues? > > > > > > Thanks > > > > Ursula > > > > -- > > Ursula Schulze-Gahmen, PhD. > > QB3, Tjian Lab > > MCB, 16 Barker Hall #3204 > > University of California Berkeley > > Berkeley, CA 94720-3204 > > Phone: (510) 642 8258 > > uschulze-gahmen(a)lbl.gov > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > >

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Re: [phenixbb] refinement of N-glycosylation
by Ralf W. Grosse-Kunstleve 24 Feb '10

24 Feb '10

> I?m quite new to crystallography and I?m refining a structure with > ASN-NAG-NAG-BMA attached and already got help from Blaine who told me how to > do it, but I?m making a small mistake somewhere and can?t figure out what > I?m doing wrong. Must be just one paranthesis or so, I guess. > > In command line just for testing I put: > > phenix.refine refine_data.mtz refine_1-coot-1FrenumberedGlu.pdb > cif_link.params BMA.cif strategy=individual_sites+individual_adp > main.number_of_macro_cycles=2 --overwrite Did you get an error message? If not, look in the .eff file for your "apply_cif" definitions. If they don't appear there something went wrong. The file name doesn't matter at all, not even the extension, but it is important that the syntax is correct. To run the syntax check only: iotbx.phil cif_link.params Ralf

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weights optimization, add hydrogens
by Ursula Schulze-Gahmen 24 Feb '10

24 Feb '10

I am refining a 2.0 A structure in Phenix using mostly the graphical interface. The maps are very good and the R factors are low (0.208/0.173). But the geometry is not so great with bond deviations of 0.208 and Angle deviations of 1.85. What is the best thing to do to try to improve the geometry. Should I try to optimize the weights? The other question is about adding hydrogens to the model. I did add them in a previous refinement cycle. After rebuilding the model in coot, most of the model still has the hydrogens in the input file for the next refinement cycle, but some residues and waters don't have hydrogens. When I tried to add hydrogens again to the model, I got an error message about atoms being to close. Does Phenix know where to add hydrogens if the input model has already hydroegns on many residues? Thanks Ursula -- Ursula Schulze-Gahmen, PhD. QB3, Tjian Lab MCB, 16 Barker Hall #3204 University of California Berkeley Berkeley, CA 94720-3204 Phone: (510) 642 8258 uschulze-gahmen(a)lbl.gov

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Phenix.ligandfit is not happy with my labels
by ucbccka 24 Feb '10

24 Feb '10

I am getting an error when trying to run phenix.ligandfit in the version phenix-1.6-289. I am trying to get it to use an mtz generated via refmac <recoils at the chorus of booooo's> and fit the ligand into the difference map. If I run phenix.ligandfit data=phaser_1.1_refmac1.mtz model=phaser_1.1_refmac1.pdb ligand=ATP.pdb It complains about my labels, saying.. ********************************* Sorry, input labels or map type unclear for phaser_1.1_refmac1.mtz For lig_map_type=pre_calculated_map_coeffs supply F and PHI (optionally FOM) (or 2FOFCWT and PH2FOFCWT) For lig_map_type=fo-fc_difference_map supply one column label for FP For lig_map_type=fobs_map supply one column label for FP Please specify which lig_map_type above you would like and also specify the necessary input column labels for your map like one of these samples: input_labels="FP" input_labels="2FOFCWT PH2FOFCWT" input_labels="FP PHIB FOM" ************************************* Looking at the documentation I tried getting PHENIX to tell me what labels it could see by running that autosol query and it kindly told me that my mtz file contained ************************ 'FreeR_flag' 'F_New' 'SIGF_New' 'FC' 'PHIC' 'FC_ALL' 'PHIC_ALL' 'FWT' 'PHWT' 'DELFWT' 'PHDELWT' 'FOM' ************************** so, I ran phenix.ligandfit data=phaser_1.1_refmac1.mtz model=phaser_1.1_refmac1.pdb ligand=ATP.pdb input_labels="DELFWT PHDELWT" and got the original message complaining that my labels are unclear. I even used the GUI, it recognises all the pairs of labels giving me the options to look at each map if I want and then..... complains that my labels are unclear. Clearly my labels are unclear, but I am now unclear how to proceed. If anyone could suggest something please then I would be most appreciative. Clearly. cheers

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Technology Specialist Position, Lawrence Berkeley National Laboratory
by Paul Adams 23 Feb '10

23 Feb '10

We are seeking a structural biologist technology specialist to research, document, and communicate new technologies to the scientific community. This project is part of the NIH-funded Protein Structure Initiative (PSI) Knowledgebase. The position requires interactions with other groups in the Knowledgebase, members of the Protein Data Bank, researchers at NIH-funded PSI centers, scientific journals, and the broader biological research community. The successful candidate will work under the direction of the Principal Investigator for this project. Primary duties and responsibilities are promoting new PSI- developed technologies to the broader scientific community, and maintaining and further developing a web portal describing these technologies. The successful candidate will need to be able to produce attractive online content, and have good scientific writing /proof reading skills. There is also a large community outreach element to the role, including presentations at meetings, the answering of questions via email, and the possibility of establishing an online forum. Additional tasks may include setting up a SVN software repository, and other online tools which will be of assistance to the structural biology community. Qualifications: B.S., M.S., Ph.D. or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using either computation or instrumentation. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Excellent spoken and written English skills are essential. Familiarity with scripting languages such as Python. Experience with maintaining web sites. To apply: visit http://cjo.lbl.gov/ and search for the keyword PSI or the job number 24114. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology 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: Patty Jimenez [ PAJimenez(a)lbl.gov ] [ 1-510-486-7963 ] --

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metal ion
by chene＠umbi.umd.edu 20 Feb '10

20 Feb '10

Dear Phenix users, My question may have been asked before. I am refining a structure containing calcium ions. I am wondering if the program considers it to be divalent Ca++ or neutral calcium atom. It seems that the ion and neutral atom have different atomic scattering factors. Thanks Chen Chen Chen, PhD, Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 240-314-6122

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Re: [phenixbb] riding model and deposition
by Alex Theodossis 19 Feb '10

19 Feb '10

Dear Pavel, thank you for your comments. Alex

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omit map with twinning?
by Kelly Daughtry 18 Feb '10

18 Feb '10

Hello all, The omit_map in the new gui (version 1.5) is great, but I can not include a twin law when calculating the omit map, thus the result is very messy unclear maps. I do not know if 1.6 has the solution or not, I am still lobbying our computer guy to upgrade to it... Is there a way from the command line i can include the twin law in autobuild so I can calculate the omit map, or can I just add it into the eff file? My other solution has been to use the create maps function with my data and pdb with ligand removed. This works, giving me a nice Fo-DFc map, but it would be nice to be able to show a true omit map for the ligand, as is customary in most structure papers I have run across. Thanks in advance for any help you can provide! Kelly ******************************************************* Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 *******************************************************

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riding model and deposition
by Alex Theodossis 18 Feb '10

18 Feb '10

Dear phenixbb, I have refined a 1.3A structure using individual anisotropic B-factors (Rfactor, 15.5%; Rfree, 17.7%). Additional use of the riding model during refinement has improvement the R values (Rf, 14.5%; Rfree, 16.6%), although bond length and angle outliers did increase (anyone know why that would be?). I have decided to deposit the model obtained using the riding model, but am unsure whether to include the hydrogen coordinates in the deposition. The Phenix.refine documentation advises that they are left in, as they are needed to reproduce the refinement statistics. However, reviewing the high resolution structures in the PDB I found that: 1. In the case of structures refined using REFMAC or SHELX, the riding model does not seem to be included, although its use during refinement is mentioned in the pdb header. 2. In the case of structures refined using PHENIX, use of the riding model is sometimes indicated in the header, but hydrogen coordinates only appear to be included in the pdb in the case of structures refined to a resolution better than 1.3A. As far as I can understand the purpose of the riding model is to provide additional restraints for refinement, so as long as its use is made evident in the pdb header (and maybe the methods section of the publication) that should be enough. Inclusion of hydrogens in the model, when you can't see them seems inappropriate. Nevertheless, I would appreciate a more authoritative perspective on this issue. Thank you in advance, Alex Theodossis

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refinement error with ligand
by Christian Roth 17 Feb '10

17 Feb '10

Dear all, I started a refinement of one of my structures using the GUI of phenix (Version 1.6). I used the options of adding hydrogens and dis a suimulated annealing. I used the output file and corrected it manually using Coot. I incorporated a few Ethylenglycol Monomers which might have bound. I merged everything wrote the file out and loaded this pdb in the GUI. I got an error which might be du to the fact that I didnt specify a CIF file for the ligand. I started ready set from the GUI to check the pdb and used REEL to create a CIF File. I added the CIF-File to the File list and tried to start again phenix.refine using the hydrogen option but no sim. annealing. However I got always the following error log: # Date 2010-02-17 Time 12:00:35 CET +0100 (1266404435.31 s) #phil __OFF__ Command line arguments: "/homes/roth/clcf/049b32mlsyncref/phenix/phenix/project_data/refine_15.eff" "-- overwrite" HOST = bbzws339 HOSTTYPE = i486-linux VENDOR = intel USER = roth PID = 29983 ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.6 Release tag: 289 Platform: intel-linux-2.6 linux User: roth ------------------------------------------------------------------------------- phenix.refine: Macromolecular Structure Refinement Monomer Library directory: "/software/linuxsoft/phenix-1.6-289/chem_data/mon_lib" Total number of atoms: 16881 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1575 Classifications: {'peptide': 94} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 87} and so on for other chains Chain: "R" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'EDO': 1} Unexpected atoms: {'EDO,HO1': 1, 'EDO,HO2': 1} Classifications: {'undetermined': 1} Number of atoms with unknown nonbonded energy type symbols: 16 "HETATM16821 HO2 EDO K 1 .*. H " "HETATM16826 HO1 EDO K 1 .*. H " "HETATM16828 HO2 EDO L 1 .*. H " "HETATM16834 HO1 EDO L 1 .*. H " "HETATM16836 HO2 EDO M 1 .*. H " "HETATM16840 HO1 EDO M 1 .*. H " "HETATM16842 HO2 EDO N 1 .*. H " "HETATM16848 HO1 EDO N 1 .*. H " "HETATM16850 HO2 EDO O 1 .*. H " "HETATM16857 HO1 EDO O 1 .*. H " ... (remaining 6 not shown) I looked in the pdb for this atoms, but I cannot find them. When I use a cif file created directly by phenix elbow using command line and when I did not use the update hydrogen button the refinement works. But the new residues as well as the EDO molecules have no hydrogens in riding positions. Do I have to remove all hydrogens and attach them again for every cycle? One Refinement runs for more then 5 hours regardless I use sim annealing or not. This seems to be very long for me. Maybe I want too many optimization steps? Could anyone explain me what goes wrong here. I am no so much experienced with phenix and now I run out of ideas. Thanks in advance Christian

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phenix.elbow and compound refinement
by YS. Chung 16 Feb '10

16 Feb '10

Dear all, I am having some difficulties in refining my compound within my structure. I was able to create the compound and the cif file using PRODRG and was able to fit it in coot perfectly fine. However, as pointed out by many users of phenix.refine, the cif file from PRODRG does not work well with phenix.refine. I have created a cif file using phenix.elbow and the refinement itself works fine. However, when I try to use the cif file from phenix elbow in coot, it pulls apart my compound and it's extremely difficult to work with. This still happens when I create the cif file using the --final_geometry option. Is there a way around this or is there something I can do? Any help will be much appreciated. Thank you, Yu Seon Chung

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refinement at 4.4 A => side chains or not
by jonathan elegheert 12 Feb '10

12 Feb '10

Dear bb, could anyone please share his/her opinion on following matter; I am refining a 4.4 A protein complex structure which I could solve using MR with the high resolution models of the separate components. I also have another 3.5 A crystal form of the complex. My question is whether or not to rebuild/leave "positionally known" side chains in the 4.4 A structure, because of course 2/3 of the time there is of course no density for it. However, a review of the PDB learnes that almost all models deposited between 4 and 5 A contain full side chains! Personally my opinion is not to include them because a model should be a representation of the information content of the experiment and thus density, but maybe that deviates from the consensus. On a more technical note: until now the trimming procedure has only sporadically led to Fo-Fc 'blobs' in the hydrophobic protein interior; are there proven modifications one has to apply to the bulk solvent model mask to avoid these even more? Thanks a lot for your insights, Jonathan -- Jonathan Elegheert Ph.D. Student Unit for Structural Biology& Biophysics http://www.lprobe.ugent.be/xray.html Lab for Protein Biochemistry and Biomolecular Engineering Department of Biochemistry& Microbiology Ghent University, Belgium e-mail: jonathan.elegheert(a)ugent.be

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multiple model refinement
by chene＠umbi.umd.edu 12 Feb '10

12 Feb '10

Hi, PHENIX users, Does anyone know if multiple model refinement is implemented in the latest version? I am using version 1.3. It was not implemented yet in that version. Thanks Chen Chen Chen, PhD, Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 240-314-6122

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iMosflm .mtz
by anon 11 Feb '10

11 Feb '10

Hi, i was under the impression Phenix (AutoSol) could handle .mtz files from iMosflm, however when i input the .mtz file into AutoSol, no labels appears in the pull-down menu, and pressing Run results in a dialogue box appearing stating you must select a column label for the reflection file, if no labels are present it may not be a valid format. If i input the iMosflm .mtz file into phenix.reflection_file_editor, and copy over the I, SIGI, M_ISYM columns, i get the following error; A Python error was detected. This is probably a bug; click "OK" to send a bug report to the PHENIX developers. TypeError : not all arguments converted during string formatting Traceback (most recent call last): File "/usr/local/phenix-1.6-289/phenix/wxGUI2/MainWindow.py", line 880, in OnRun self.run() File "/usr/local/phenix-1.6-289/phenix/wxGUI2/Programs/ HKLTools.py", line 81, in run symmetry_callback=None) # TODO File "/usr/local/phenix-1.6-289/cctbx_project/iotbx/ reflection_file_editor.py", line 358, in __init__ "related reflections are not identical.)" % array_name) TypeError: not all arguments converted during string formatting When i use the scaled .mtz file produced by scala, AutoSol works fine. Just wondering what's going on! Also, how do you delete individual Jobs in the Job History window (ie jobs that have failed or you no longer want to keep etc) Thanks for the help

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phenix.refine frozen
by Roberto Steiner 11 Feb '10

11 Feb '10

Hi there, I would appreciate some feedback on the following: I am playing around with phenix.refine which comes with Phenix distro 1.6-289 for Mac-Intel. When running a normal refinement job (ind site + grouped ADPs + ncs+TorsionSimulatedAnnealing) phenix.refine gets stuck after bulk solvent modelling and scaling. The last things I see in the log page are: ====================== bulk solvent modeling and scaling ====================== |--(resolution: 3.50 - 58.55 A; n_refl. = 55140)------------------------------| | | | r_work= 0.2687 r_free= 0.2800 ksol= 0.38 Bsol= 10.09 scale= 1.148 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-2.67,-2.67,5.34,0.00,0.00,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.41 A | | x-ray target function (ml) for work reflections: 7.216427 | | -----------------------------------------------------------------------------| ========================== Target weights: x-ray data ========================= and that's it. For completeness, I must report that I changed the defaults of wxc_scale and wxu_scale (but surely that cannot be the problem...). Switching off the TorsionSimAnnealing does not help. Additionally, if I click on the abort button on the bottom-left of the page nothing happens. On the other hand if I click on the abort icon at the top of the page I get the message "You are not currently running any calculations. Do you want to close this window?" If I say Ok the following message appears: "There is at least one process running; are you sure you want to exit before it is finished" Other tasks (phenix.xtriage for example) seem to run fine. Any suggestion? Best Roberto

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phenix.model_vs_data or something else for 'most disagreeable reflections' ?
by Francis E Reyes 11 Feb '10

11 Feb '10

Hi phenixer's I'm looking for a utility that'll calculate Fc given a refined model and compare it to Fo not on a global scale, but on an individual reflection scale. ShelX does this a reflection list of 'most disagreeable reflections'. Is this possible in phenix? Or another utility (besides shelx)? thanks FR --------------------------------------------- Francis 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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Re: [phenixbb] Omit map Problem
by Carruthers, Carl W. 10 Feb '10

10 Feb '10

Coot works fine. When I click the GUI button after the run, it loads the pdb file that I used as a start model and nothing else. When I try opening the composite map manually (using coot: "open mtz", "auto open mtz" or even "open map" ) it says at the bottom "read map /file path/ resolve_composite_map.mtz failed." Thanks again! Carl Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Omit map Problem
by Carruthers, Carl W. 10 Feb '10

10 Feb '10

When making an composite omit map in Phenix 1.6 GUI, the final "resolve_composite_map.mtz" file won't load in coot or pymol. When I click the little magnifying glass on the Summary page, Phenix states that it can't find the file, even though I can see it when using Finder (Mac OS). The final lines of the run status are below: Putting all omit results in AutoBuild_run_61_/OMIT OMIT results in AutoBuild_run_61_/OMIT : ['overall_best.pdb_OMIT_REGION_1', 'overall_best.pdb_OMIT_REGION_10', 'overall_best.pdb_OMIT_REGION_11', 'overall_best.pdb_OMIT_REGION_12', 'overall_best.pdb_OMIT_REGION_2', 'overall_best.pdb_OMIT_REGION_3', 'overall_best.pdb_OMIT_REGION_4', 'overall_best.pdb_OMIT_REGION_5', 'overall_best.pdb_OMIT_REGION_6', 'overall_best.pdb_OMIT_REGION_7', 'overall_best.pdb_OMIT_REGION_8', 'overall_best.pdb_OMIT_REGION_9', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_1', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_10', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_11', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_12', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_2', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_3', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_4', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_5', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_6', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_7', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_8', 'overall_best_denmod_map_coeffs.mtz_OMIT_REGION_9', 'resolve_composite_map.mtz'] Combining all 12 omit regions in AutoBuild_run_61_/OMIT No background map in composite map Composite omit result is in /Users/carlcarruthers/Crystallography/AutoBuild_run_61_/OMIT/resolve_composite_map.mtz Possible operation: finished Required antecedents: [] Expected results: [] Application method: finished Yes, have antecedents... Resulting expectation:10000.0 Am I doing something wrong? Is it a bug? Thanks for helping a crystallogaophy newb (this is my first model!)... Carl Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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