- phenixbb - phenix-online.org

Re: [phenixbb] s_annealing within AutoBUILD
by Nicholas Noinaj 14 Jul '06

14 Jul '06

Tom, I know during the first build cycle, it worked. Later on, I noticed that it reset s_annealing to false again, as you probably anticipated. I will make the additional changes in the morning and let you know how it goes. Thanks again! Cheers, Nick -----Original Message----- From: "Thomas C. Terwilliger" <terwilliger(a)lanl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Date: Fri, 14 Jul 2006 17:18:05 -0600 (MDT) Subject: Re: [phenixbb] s_annealing within AutoBUILD Hi Nick, Great. In testing this, I found there is one more thing to do to make the simulated annealing actually happen: Edit the file $PHENIX/phenix/phenix/autosol/run_phenix_refine.py at line 144 from self.params.refinement.simulated_annealing.do_simulated_annealing=True to: self.params.refinement.main.simulated_annealing=True (don't change the indentation or anything, just the text). Ralf: can you possibly verify that this is the correct current syntax? This will in fact do SA refinement once per build cycle, just as you originally asked for. Thanks! -Tom T > Tom, > > made the changes to AutoBuild.py, works like a charm now! Thanks! > > > > cheers, > Nick > > > > > ----- Original Message ----- > From: "Tom Terwilliger" <terwilliger(a)lanl.gov> > To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> > Sent: Friday, July 14, 2006 4:58 PM > Subject: Re: [phenixbb] s_annealing within AutoBUILD > > >> Hi Nick, >> >> Oops. I didn't recheck to make sure it comes up. It should have but >> doesn't. I left it off the menu I'm afraid. >> -Tom T >> >> ps. If you want to be adventurous, go to the file >> >> $PHENIX/phenix/phenix/wizards/AutoBuild.py >> >> First copy the file to AutoBuild.py.orig to be safe, then >> >> edit line 3342 from: >> >> 'start_chains_list','two_fofc_in_rebuild','input_labels', >> >> to say instead >> >> >> 'start_chains_list','two_fofc_in_rebuild','input_labels','s_annealing', >> >> and then close the wizard and open it again. This adds s_annealing to >> the >> menu and hopefully should cure the problem. >> >> I'm sorry about that! >> -Tom T >> >> At 04:48 PM 7/14/2006 -0400, you wrote: >>>Tom, >>> >>> I thought that I just overlooked the s_annealing parameter, but this >>>doesn't seem to be the case. I don't seem to have this parameter in my >>>list. I am using the latest version of PHENIX loaded onto a LINUX >>>workstation. >>> >>>Could it be that the parameter is missing or that I may have missed >>>something during the installation, since I am a newbie to Linux? >>> >>>Thanks again in advance for all your help! >>> >>> >>>Cheers, >>>Nick >>> >>> >>> >>> >>> >>>----- Original Message ----- >>>From: "Tom Terwilliger" <terwilliger(a)lanl.gov> >>>To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> >>>Sent: Friday, July 14, 2006 4:20 PM >>>Subject: Re: [phenixbb] s_annealing within AutoBUILD >>> >>> >>> > Hi Nick, >>> > >>> > Yes, you can modify the parameter "s_annealing" by going to the menu >>> at >>> > the >>> > bottom right corner of the Parameters (inputs) screen labelled >>> > >>> > SET VARIABLE (Advanced users) >>> > >>> > and selecting "s_annealing" >>> > >>> > then click "CONTINUE" and a screen will come up allowing you to >>> choose >>> > Yes >>> > or No to s_annealing. Then when you click CONTIUE the wizard will >>> > continue >>> > whatever it was doing. >>> > >>> > You can set this variable when you are setting up your run; do it any >>> > time >>> > before the last screen comes up. >>> > >>> > All the best, >>> > Tom t >>> > >>> > At 03:54 PM 7/14/2006 -0400, Noinaj wrote: >>> >>Hi, >>> >> >>> >> >>> >>I am running AUTOBUILD on a friend's structure, and noticed in the >>> log >>> >>file the s_annealing parameter set to false. Is it possible to set >>> >>this >>> >>parameter to true when doing an AUTOBUILD run, say to do s_a after >>> each >>> >>build cycle? I have read that I can use phenix.refine at the command >>> >>line >>> >>to run s_annealing, but didn't know if I could modify this option >>> >>within >>> >>the wizards. I checked out the list of parameters which I am allowed >>> >>to >>> >>change, but didn't see s_anneal anywhere. >>> >> >>> >>Thanks for all replies in advance! >>> >> >>> >> >>> >> >>> >>Cheers, >>> >>Nick >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >>________________________________________ >>> >> >>> >>Nicholas Noinaj >>> >>University of Kentucky School of Medicine >>> >>Department of Molecular and Cellular Biochemistry >>> >>Biomedical Biological Sciences Research Building, Rm 236 >>> >>741 S. Limestone >>> >>Lexington, Ky 40536 >>> >>Lab: 859-323-8183 >>> >>Home: 859-228-0978 >>> >><mailto:[email protected]>noinaj(a)uky.edu >>> >>www.noinaj.com >>> >> >>> >> >>> >>_______________________________________________ >>> >>phenixbb mailing list >>> >>phenixbb(a)phenix-online.org >>> >>http://www.phenix-online.org/mailman/listinfo/phenixbb >>> > >>> > >>> > >>> > >>> > Thomas C. Terwilliger >>> > Mail Stop M888 >>> > Los Alamos National Laboratory >>> > Los Alamos, NM 87545 >>> > >>> > Tel: 505-667-0072 email: terwilliger(a)LANL.gov >>> > Fax: 505-665-3024 SOLVE web site: >>> http://solve.lanl.gov >>> > PHENIX web site: http:www.phenix-online.org >>> > ISFI Integrated Center for Structure and Function Innovation web >>> site: >>> > http://www.techcenter.mbi.ucla.edu >>> > TB Structural Genomics Consortium web site: http://www.tbgenomics.org >>> > >>> > _______________________________________________ >>> > phenixbb mailing list >>> > phenixbb(a)phenix-online.org >>> > http://www.phenix-online.org/mailman/listinfo/phenixbb >>> > >>> >>>_______________________________________________ >>>phenixbb mailing list >>>phenixbb(a)phenix-online.org >>>http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> >> >> >> Thomas C. Terwilliger >> Mail Stop M888 >> Los Alamos National Laboratory >> Los Alamos, NM 87545 >> >> Tel: 505-667-0072 email: terwilliger(a)LANL.gov >> Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov >> PHENIX web site: http:www.phenix-online.org >> ISFI Integrated Center for Structure and Function Innovation web site: >> http://www.techcenter.mbi.ucla.edu >> TB Structural Genomics Consortium web site: http://www.tbgenomics.org >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb ________________________________________ Nicholas Noinaj University of Kentucky School of Medicine Department of Molecular and Cellular Biochemistry Biomedical Biological Sciences Research Building, Rm 236 741 S. Limestone Lexington, Ky 40536 Lab: 859-323-8183 Home: 859-228-0978 noinaj(a)uky.edu www.noinaj.com

1 0

Re: [phenixbb] s_annealing within AutoBUILD
by Ralf W. Grosse-Kunstleve 14 Jul '06

14 Jul '06

> self.params.refinement.main.simulated_annealing=True > > (don't change the indentation or anything, just the text). > > Ralf: can you possibly verify that this is the correct current syntax? Yes, it is correct.

1 0

s_annealing within AutoBUILD
by Noinaj 14 Jul '06

14 Jul '06

Hi, I am running AUTOBUILD on a friend's structure, and noticed in the log file the s_annealing parameter set to false. Is it possible to set this parameter to true when doing an AUTOBUILD run, say to do s_a after each build cycle? I have read that I can use phenix.refine at the command line to run s_annealing, but didn't know if I could modify this option within the wizards. I checked out the list of parameters which I am allowed to change, but didn't see s_anneal anywhere. Thanks for all replies in advance! Cheers, Nick ________________________________________ Nicholas Noinaj University of Kentucky School of Medicine Department of Molecular and Cellular Biochemistry Biomedical Biological Sciences Research Building, Rm 236 741 S. Limestone Lexington, Ky 40536 Lab: 859-323-8183 Home: 859-228-0978 noinaj(a)uky.edu www.noinaj.com

5 8

sa
by Tom Terwilliger 14 Jul '06

14 Jul '06

Hi again Nick, I should add that the SA option applies (unfortunately) to all refinements, there is no option at present to only do SA once per cycle as you were looking for. All the best, Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://www.techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.tbgenomics.org

3 3

Re: [phenixbb] How to use phenix for SAD data
by Petrus H Zwart 10 Jul '06

10 Jul '06

> I used the format ccp4 unmerged i.e the direct output of the > mosflm after integration. Please use Scala or other software for scaling and merging your integrated data. When that is done, you should be okai. Regarding 'proper' use of the wizard/gui, try of of the examples in the example directory. Running those shuold give you a feeling of what needs to be done. The examples should work. Most parameter fields have an associated info string that explains briefly what is expected. HTH Peter

1 0

How to use phenix for SAD data
by pramod＠cdfd.org.in 10 Jul '06

10 Jul '06

Hi all i am using the Phenix-GUI first time ,for solving the sad data. I processed my raw data with the mosflm.Further output of the mosflm were used for getting other information or working through this data.so, i started with the strteiges of solve through mad. after setinmg up all the anamolous parameters ,this is always displaying red in the very first in the setup anamolous data gui with the information that format error.i used the format ccp4 unmerged i.e the direct output of the mosflm after integration.i also used the conversion of mtz file into hkl through ccp4 scaling and merging intensities-in which one option i used is the get output as unmerged intensities but, that also didnot worked. suggestions will be appreciated and also i want the deatiled information about how to use the phenix gui properly. with regards Pramod Kumar Junior Research Fellow c/o-Dr.Shekher C Mande Center for DNA Fingerprinting and Diognostics ECIL road Nacharam Hyderabad-76 -

2 1

System requirement
by 崔中利 10 Jul '06

10 Jul '06

Dear all, I am trying to run phenix on a IBM X-31 laptop (1.3G CPU, 256M memory, redhat Fedora Core 3 operation system). But every time it ceased midway. So, can somebody tell me the system requirement to run Phenix? or is any other software required to run Phenix? Zhongli

2 1

Problem on Running Phenix
by 崔中利 06 Jul '06

06 Jul '06

Dear All, I have just installed phenix 1.24.1b and tested my data on this version of Phenix. I tried Autosol. There should be 4 windows to finish the parameter setup according to the documents. But I met a problem after setting the pathway of file of protein sequence (2nd window). The window didn't change to green after I set the pathway and pressed Continue. But from the CPU indicator I knew it was running (100% CPU occupation). And from the log file, I found the program set the resolution automaticlly (3rd window). But after serveral hours' running, I get nothing. What's more, the running sequence was a bit different to the online document of Phenix. The setup window (1st window) appeared first, then the Autosol program window. I don't know what wrong happened to my running, problem of software or my computer. Zhongli

1 0

AUTOBUILD CC
by Noinaj 06 Jul '06

06 Jul '06

Hi, I am new to PHENIX and would like to get a bit of guidance. I am helping a friend with her structure using SAD phasing. She has 4 Se/molecule with 4 mol/ASU. We used Solve to find her sites with nice occupancy, and then ran AUTOBUILD, just to see how it did. It is returning map correlation coeff, Z-scores, etc. What are good numbers for these parameters? Thanks in advance. Cheers, Nick

2 2

Re: [phenixbb] problem when installing phenix 1.24.1b
by Petrus H Zwart 06 Jul '06

06 Jul '06

This most likely means you have downloaded the binairies that do not match your machine architecture. See the readme file: ------------------------------------------------------------------------ ----------- Currently, the following Redhat Linux platforms are tested, and therefore supported for the distribution: - Redhat 8.0 - Redhat 9.0 - Redhat Enterprise Workstation 3 [+/- x86_64] - Redhat Enterprise Server 4.2 [+/- x86_64] - Fedora Core 3 [+/- x86_64] - Fedora Core 5 [+/- x86_64] Redhat versions prior to 8.0 are not supported. PHENIX should also install on other Linux platforms such as Mandrake, or SuSe. There are 4 different Linux installations available, based on the version of the kernel (2.4 or 2.6) and the CPU type (ix86 or x86_64). If it isn't clear which you need then type this command on the machine in question: % uname -rm The first item is the kernel version, the second is the machine hardware. Please download the appropriate installer based on this table: ------------------------------------------------------------------------ - | hardware \ kernel | 2.4 | 2.6 | ------------------------------------------------------------------------ - | ix86 | intel-linux-2.4 | intel-linux-2.6 | ------------------------------------------------------------------------ - | x86_64 | intel-linux-2.4-x86_64| intel-linux-2.6- x86_64| ------------------------------------------------------------------------ - Currently, the following other Unix platforms are tested, and therefore supported for the distribution: - Compaq Tru64 5.1 - SGI Irix 6.5[*] ------------------------------------------------------------------------ ------------ i.e., check if if you have a 2.4 or 2.6 linux kernel and what your cpu type is. for me, I get this: 2.6.11-1.1369_FC4smp i686 i.e, i need the 2.6 , ix86 version. HTH Peter Hi, I met a problem when installing the phenix 1.24.1a. The installer gave me an error information "neither source nor binary availabe, exiting installation". What's wrong with my installation? Zhongli _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

1 0

problem when installing phenix 1.24.1b
by 崔中利 06 Jul '06

06 Jul '06

Hi, I met a problem when installing the phenix 1.24.1a. The installer gave me an error information "neither source nor binary availabe, exiting installation". What's wrong with my installation? Zhongli

1 0

run phenix in vitue linux environment
by 崔中利 05 Jul '06

05 Jul '06

I installed phenix 1.1a in a virtue Fedora Core 3 machine with VMware workstation 5 under windows XP on a IBM X31 notebook. When I run autosol (sad) to solve my protein, the system gave me error information "the connection to strategy disrupted" after all parameters are set, but it seems that the program is still running (for the window is still green) . However, the Autosol is showed as Finished in Job control window. Even if I leave the program running overnight, there is no solution produced. Can anyome give me some comments? Zhongli

1 0

PHENIX 1.24.1 beta now available
by Paul Adams 05 Jul '06

05 Jul '06

======================================================================= PHENIX 1.24.1 Beta Release ======================================================================= On behalf of the PHENIX development team I am happy to announce that the next general release version of PHENIX is now available. Binary installers for Linux, SGI and Tru64 platforms are available at our download site: http://phenix-online.org/download/ Current users of PHENIX should upgrade to this most recent release version. To obtain download instructions visit: http://phenix-online.org/phenix_request/ Documentation for PHENIX is available at: http://phenix-online.org/download/documentation/phenix/ There is a PHENIX mailing list at: http://www.phenix-online.org/mailman/listinfo/phenixbb/ There is a PHENIX wiki at: http://www.phenix-online.org/phenix_wiki Please consult the installer README file or online documentation for installation instructions. This is a beta test version, and we therefore look forward to feedback and bug reports from users. Please direct questions and problem reports to: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to PHENIX should visit the PHENIX website for information about the PHENIX Industrial Consortium: http://www.phenix-online.org/ This version of PHENIX has three main user interfaces: command-line tools, strategies and wizards. Wizards are available under the Wizard tab in the PHENIX GUI, and are designed to complete a complex structure determination process, making automatic decisions when possible, but prompting the user for additional information when necessary. Strategies are available under the Strategy tab in the PHENIX GUI, and are networks of tasks constructed to perform higher-level functions. Version 1.24.1b of PHENIX includes: Wizards (in the PHENIX GUI and from the command-line) ===================================================== - AutoSol - automated structure solution (from processed data to a first map and model) using HySS, SOLVE, RESOLVE, and phenix.refine. - AutoMR - automated molecular replacement, using PHASER. Followed by automated model rebuilding using the AutoBuild wizard. - AutoBuild - automated model building or rebuilding combined with structure refinement, using RESOLVE and phenix.refine. - AutoLig - automated ligand fitting into difference density maps using RESOLVE once a complete protein model is available. Strategies (in the PHENIX GUI) ============================== - Ligand screening against the top 200 ligands in the PDB, using RESOLVE. - Structure solution (MAD/SAD and SIR(AS)/MIR(AS)) combining HySS, SOLVE and RESOLVE. - Phase improvement using maximum likelihood methods in RESOLVE. - Model building using TEXTAL or RESOLVE. Command-line tools ================== - mmtbx.xtriage (comprehensive data quality assessment, including twin analysis) - iotbx.reflection_statistics (analysis of diffraction data) - mmtbx.fest (FA value calculation) - phenix.hyss (anomalous substructure determination) - textal.build (automated model building with TEXTAL) - elbow.builder (generation of ligand coordinates and restraints) - phenix.refine (automated structure refinement) - phenix.geometry_minimization (regularize a structure) - phenix.solve (solve) - phenix.resolve (resolve) - phenix.resolve_pattern (resolve_pattern) - iotbx.mtz.dump (write useful information about a MTZ file) - iotbx.pdb.hierarchy (write useful information about a PDB file) Citing PHENIX ============= If you use PHENIX for solving a structure please cite this publication: PHENIX: building new software for automated crystallographic structure determination P.D. Adams, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter and T.C. Terwilliger. Acta Cryst. D58, 1948-1954 (2002). PHENIX Developers ================= Lawrence Berkeley National Laboratory - Paul D. Adams - Pavel Afonine - Ralf W. Grosse-Kunstleve - Nigel W. Moriarty - Nicholas K. Sauter - Peter H. Zwart Los Alamos National Laboratory - Tom C. Terwilliger - Li-Wei Hung - Thiru Radhakannan University of Cambridge - Randy J. Read - Airlie J. McCoy - Laurent C. Storoni Texas A&M University - Jim C. Sacchettini - Tom R. Ioerger - Kresha Gopal - Lalji Kanbi - Erik McKee - Reetal K. Pai - Tod D. Romo - Jacob N. Smith Acknowledgements ================ We are very grateful to the following for making code or libraries available to us: - Alexei Vagin and Garib Murshudov for the CCP4 Monomer Library. - The CCP4 developers for making the MTZ library available to us. - Kevin Cowtan for contributing to the cctbx reciprocal space asymmetric units. - David Abrahams for developing the Boost.Python library. Funding ======= The development of PHENIX is principally funded through the Protein Structure Initiative of the National Institute of General Medical Sciences (NIH) under grant P01GM063210. For further information about the Protein Structure Initiative please visit: http://www.nigms.nih.gov/psi/ We also acknowledge the generous support of the members of the PHENIX Industrial Consortium. For more details please visit: http://www.phenix-online.org/ ======================================================================= PHENIX 1.24.1 Beta Release ======================================================================= -- ========================================================== | Paul Adams, | | Senior Staff Scientist, Physical Biosciences Division | | Head, Berkeley Center for Structural Biology | | Deputy PI, Berkeley Structural Genomics Center | |--------------------------------------------------------| | Building 64, Room 248 | Lawrence Berkeley Laboratory, | | Tel: 510-486-4225 | 1 Cyclotron Road, | | FAX: 510-486-5909 | BLDG 64R0121, | | mailto:[email protected] | Berkeley, CA 94720, USA. | ==========================================================

3 4

New version of Phenix
by 崔中利 05 Jul '06

05 Jul '06

Dear administrator, I have seen the introduction to 1.24.1 beta version of phenix. Why is it still not avalable for download? What is the improvement comparing to version 1.1 alpha? Zhongli

1 0

Problem with remotely displaying PHENIX
by Luca Jovine 01 Jun '06

01 Jun '06

Dear all, While waiting for a Mac OS X version of PHENIX, I have installed it on a Linux server, with the idea of remotely display the GUI on our OS X machines. However, when I try to do so, the GUI briefly opens and then bombs out with the following message: LINUX> phenix Running the PHENIX GUI with /home/xray/luca/bin/phenix/phenix-1.1a/phenix-1.1a/ build/intel-linux/python/bin/python PHENIX distribution located in /home/xray/luca/bin/phenix/ phenix-1.1a/phenix-1.1a/phenix Variable SSH_PATH set to /usr/bin/ssh Variable PYMOL_PATH set to /home/xray/luca/bin/phenix/ phenix-1.1a/phenix-1.1a/pymol Variable RSH_PATH set to /usr/bin/rsh Project Details Project Name: luca Date Stamp : Thu Jun 01 15:56:23 2006 Machine : localhost Directory : /home/xray/luca PDS Server will be on ---------- localhost (localhost) ---------- /home/xray/luca ---------- Port 28537 PID 25355 PDS Server Details User : luca Machine : localhost Directory : /home/xray/luca Port : 28537 PID : 25374 Creating new Data Storage /home/xray/luca/strategies The program 'wxPhenix.py' received an X Window System error. This probably reflects a bug in the program. The error was 'BadWindow (invalid Window parameter)'. (Details: serial 6349 error_code 3 request_code 38 minor_code 0) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) ...has anyone else encountered the same issue, and, if so, managed to solve it? Thanks in advance and best regards, Luca ----------------------------------------------------- Luca Jovine, Ph.D. Karolinska Institutet Department of Biosciences and Nutrition Center for Structural Biochemistry (CSB) Hälsovägen 7, S-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6089-290 E-mail: luca.jovine(a)biosci.ki.se W3: http://www.biosci.ki.se/groups/ljo/ -----------------------------------------------------

2 1

HKL2000 and Phenix?
by ckielkop 23 May '06

23 May '06

Hi, I wonder if anyone else has had trouble running both Phenix and HKL2000 on the same linux workstation? Once Phenix we have installed and used Phenix, the HKL2000 cr_info license becomes invalid, and vice versa. A linux guru suggested in passing that our bash system has a 'license' file that gives the directories of the licenses somewhere, and that this file needs both license directories added explicitly. But where would this file be? Thanks for the help! Clara

2 1

TEXTAL Model from map
by Andrzej LYSKOWSKI 09 May '06

09 May '06

Hi, I have one question and one problem. TEXTAL expects map in X-PLOR format but what kind of map? One can make a number of different maps in CCP4 (simple, mFo-nFc, etc.). Which type make TEXTAL happy? I've tried to run 'Build Complete Model from map' strategy and what ever I do it seems to get stuck at: Stitching and Filtering C-alpha chains... - simply nothing happens anymore. What could be a problem? Just to mention it does build a model when I use '... from mtz' strategy. MfG, Andrzej -- < Andrzej Lyskowski (andrzej[dot]lyskowski[at]uni-graz[dot]at) < Chemistry Institute - Phys. Chem./Structural Biology < Heinrichstrasse 28 < A-8010 Graz, Austria < Tel.: 43 316 380 54 69 < Fax.: 34 316 380 98 50 > A designer knows he has achieved perfection > not when there is nothing left to add, > but when there is nothing left to take away. > Antoine de Saint-Exupery

3 2

Judging AutoSol Output
by agb838＠mail.usask.ca 30 Apr '06

30 Apr '06

I have some basic questions about the output from Phenix. Basically I have a data set that gave a solution, but I am not exactly sure how to tell about the quality of the solution from the outputs. The overall score is 110. I am not sure exactly what that refers to or how good/bad it is. I have attached the AutoSol.output file. Any basic suggestions at what I should be looking at, or if this is even the right file, would be helpful. The resolve.mtz and resolve.pdb look alright. They are a good start, but much improvement is needed. If anyone has some suggestions as to how to improve the output, that would also be helpful. I have also run the data through solve/resolve through the command prompt and it repeatedly locates four heavy atom sites (the data set is SAD). Yet, when Phenix is used, 16 sites are found. Why the difference and how do I tell what is working better and why. Thank you, Angela Hoffort

2 1

Re: [phenixbb] Judging AutoSol Output
by Petrus H Zwart 30 Apr '06

30 Apr '06

----- Original Message ----- From: agb838(a)mail.usask.ca Date: Monday, April 24, 2006 3:18 pm Subject: [phenixbb] Judging AutoSol Output > I have some basic questions about the output from Phenix. > Basically I > have a data set that gave a solution, but I am not exactly sure > how to > tell about the quality of the solution from the outputs. The overall > score is 110. I am not sure exactly what that refers to or how > good/badit is. I have attached the AutoSol.output file. Any basic > suggestions at > what I should be looking at, or if this is even the right file, > would be > helpful. The resolve.mtz and resolve.pdb look alright. They are a good > start, but much improvement is needed. If anyone has some > suggestions as > to how to improve the output, that would also be helpful. > > I have also run the data through solve/resolve through the command > prompt and it repeatedly locates four heavy atom sites (the data > set is > SAD). Yet, when Phenix is used, 16 sites are found. Why the difference > and how do I tell what is working better and why. > Autosol is finding sites using HySS and subsequently iterates phasing, solvent flattening with the use of difference maps to find more sites. Juding from your output, it find most sites in 1 go. If you want to compare sites you find by Solve, Hyss, or famous programs from Buffalo or Goettingen, use iotbx.emma ha_from_autosol.pdb other.pdb To get an idea how many sites are matching. As far as I understand it, the overall score is a score relative to the other hand and other solutions and its absolute value is not so important, as long as it is (much) larger that any other solution. In your case, solution 1 has a score of 110, solution has a solution of 63. It is also finding NCS, which seems to be good (NCS correlation of 0.66 early no allready). Improvement of the pdb file is obtained by runnnig the modelbuild wizard I think. The Autosol wizard only carries out a limit number of model building cycles and the modelbuild wizard does a more thorough job. HTH Peter _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

1 0

phenix.refine Crashes with "ZeroDivisionError: float division"
by Dale Tronrud 14 Apr '06

14 Apr '06

Hi, I'm new to phenix and phenix.refine. I am trying to refine a protein with phenix.refine but the program crashes quite quickly. I have appended all of the output below, but the critical part is (I believe): File "/usr/local/phenix-1.1a/cctbx/cctbx/miller.py", line 432, in auto_anomalous anomalous_flag = (2*self.n_bijvoet_pairs()/self.indices().size() ZeroDivisionError: float division Apparently, self.indices().size() is zero, but I don't know why or really what that is. My mtz file does not contain any anomalous data. It just has F, SigF, and a free R flag for the positive octant of data. (Well, since this is P6122 the positive duodecant.) Any advise would be appreciated. Dale Tronrud # Date 2006-04-14 Time 15:14:52 PDT -0700 #phil __OFF__ ------------------------------------------------------------------------------ PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.1a Platform: intel-linux linux User: dale ------------------------------------------------------------------------------ phenix.refine: Macromolecular Structure Refinement ------------------------------------------------------------------------------ Phenix developers include: P.D. Adams, P. Afonine, K. Gopal, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.K. Pai, R.J. Read, T.D. Romo, J.C. Sacchettini, N.K. Sauter, L.C. Storoni, T.C. Terwilliger Phenix home page: http://www.phenix-online.org/ ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Phenix components are copyrighted by: - Lawrence Berkeley National Laboratory - Los Alamos National Laboratory - University of Cambridge - Texas Agricultural Experiment Station & Texas Engineering Experiment Station ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Major third-party components of Phenix include: Python, wxPython, Boost, SCons, Clipper, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS Enter phenix.acknowledgments for details. ------------------------------------------------------------------------------ Processing inputs. This may take a minute or two. Crystal symmetry: Unit cell: (93.016, 93.016, 130.096, 90, 90, 120) Space group: P 61 2 2 (No. 178) phs1rb-coot-1-no-peak.pdb Total number of atoms: 2733 Number of models: 1 Model: 0 Number of conformers: 3 Conformer: "A" Number of atoms: 2723 Number of chains: 5 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} Number of residues, atoms: 315, 2389 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 306, 'PCIS': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan2': 1, 'GLN:plan1': 3, 'GLN:plan2': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Number of residues, atoms: 6, 11 Unusual residues: {' ZN': 1, ' CA': 4} Inner-chain residues flagged as termini: ['ALA, ,316, , '] Classifications: {'unknown': 5, 'peptide': 1} Modifications used: {'COO': 1} Link IDs: {None: 5} Number of residues, atoms: 299, 299 Classifications: {'water': 299} Link IDs: {None: 298} Conformer: "B" Number of atoms: 2723 Common with "A": 2718 Number of chains: 5 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} bond proxies already assigned to first conformer: 12 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} bond proxies already assigned to first conformer: 12 Number of residues, atoms: 315, 2389 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 306, 'PCIS': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan2': 1, 'GLN:plan1': 3, 'GLN:plan2': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 2442 Number of residues, atoms: 6, 11 Unusual residues: {' ZN': 1, ' CA': 4} Inner-chain residues flagged as termini: ['ALA, ,316, , '] Classifications: {'unknown': 5, 'peptide': 1} Modifications used: {'COO': 1} Link IDs: {None: 5} bond proxies already assigned to first conformer: 5 Number of residues, atoms: 299, 299 Classifications: {'water': 299} Link IDs: {None: 298} Conformer: "C" Number of atoms: 2723 Common with "A": 2718 Common with "B": 2718 Number of chains: 5 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} bond proxies already assigned to first conformer: 12 Number of residues, atoms: 1, 12 Unusual residues: {'GLC': 1} Classifications: {'unknown': 1} bond proxies already assigned to first conformer: 12 Number of residues, atoms: 315, 2389 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 306, 'PCIS': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan2': 1, 'GLN:plan1': 3, 'GLN:plan2': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 2442 Number of residues, atoms: 6, 11 Unusual residues: {' ZN': 1, ' CA': 4} Inner-chain residues flagged as termini: ['ALA, ,316, , '] Classifications: {'unknown': 5, 'peptide': 1} Modifications used: {'COO': 1} Link IDs: {None: 5} bond proxies already assigned to first conformer: 5 Number of residues, atoms: 299, 299 Classifications: {'water': 299} Link IDs: {None: 298} Time building chain proxies: 12.22, per 1000 atoms: 4.47 Traceback (most recent call last): File "/usr/local/phenix-1.1a/phenix/phenix/command_line/refine.py", line 5, in ? command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.1a/phenix/phenix/refinement/command_line.py", line 35, in run log=log) File "/usr/local/phenix-1.1a/phenix/phenix/refinement/command_line.py", line 128, in __init__ reflection_file_server = self.reflection_file_server() File "/usr/local/phenix-1.1a/phenix/phenix/refinement/command_line.py", line 337, in reflection_file_server err=self.log) File "/usr/local/phenix-1.1a/iotbx/iotbx/reflection_file_utils.py", line 303, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.1a/iotbx/iotbx/reflection_file_reader.py", line 160, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.1a/iotbx/iotbx/mtz/__init__.py", line 363, in as_miller_arrays dataset=dataset) File "/usr/local/phenix-1.1a/iotbx/iotbx/mtz/__init__.py", line 495, in group_columns observation_type=observation_type)) File "/usr/local/phenix-1.1a/iotbx/iotbx/mtz/__init__.py", line 516, in column_group indices=group.indices).auto_anomalous(min_fraction_bijvoet_pairs=2/3.) File "/usr/local/phenix-1.1a/cctbx/cctbx/miller.py", line 432, in auto_anomalous anomalous_flag = (2*self.n_bijvoet_pairs()/self.indices().size() ZeroDivisionError: float division

1 0

Passing keyword to a Wizard
by Andrzej LYSKOWSKI 24 Mar '06

24 Mar '06

Hi, I'm getting a feedback from AutoBuild Wizard that I should set it with coarse_grid keyword (info from LAST.LOG). However, this keyword isn't present in Set Variable menu. How can set it? Regards, Andrzej -- < Andrzej Lyskowski (andrzej[dot]lyskowski[at]uni-graz[dot]at) < Chemistry Institute - Phys. Chem./Structural Biology < Heinrichstrasse 28 < A-8010 Graz, Austria < Tel.: 43 316 380 54 69 < Fax.: 34 316 380 98 50 > A designer knows he has achieved perfection > not when there is nothing left to add, > but when there is nothing left to take away. > Antoine de Saint-Exupery

2 1

Re: [phenixbb] PHENIX installation issues
by Ralf W. Grosse-Kunstleve 14 Mar '06

14 Mar '06

> > Another thing is i installed in a user so whenever i do project it > gives permission denied . I suspect you have the following situation: drwx------ 2 rwgk cci 4096 Mar 14 10:47 phenix-1.1a I.e. when you installed phenix the "umask" was set such that "group" and/or "others" don't have read permission. Please verify my suspicion with ls -d $PHENIX If you see the "drwx------" or maybe "drwxr-x---" it is easy to fix. Use the su command to become root, then: find phenix-1.1a -exec chmod go+r {} \; find phenix-1.1a -type d -exec chmod go+x {} \; Cheers, Ralf

1 0

PHENIX installation issues
by Peter Zwart 14 Mar '06

14 Mar '06

I see. Unfortunately, the switching between bash and csh is needed until the next release. I am not quite sure what this > Another thing is i installed in a user so whenever i do project it gives permission denied . error/problem exactly is or how it can be solved, but maybe some of my collegues have an idea. Peter Ethayathulla Abdulsamath wrote: > hi Petrus: > > yes, it got installed I replied in phenixbb. > > But problem is everytime i have to do csh then source phenix_env file. > Then again change back to bash. > > Another thing is i installed in a user so whenever i do project it > gives permission denied . > > Everytime i logged in root then do thinz IS there any sol for it >

1 0

Re: [phenixbb] phenixbb Digest, Vol 4, Issue 5
by Ralf W. Grosse-Kunstleve 13 Mar '06

13 Mar '06

> > how to change bash setup ot csh. > > I guess you can change shell (type csh or so) in a single window for > installing, sourcing Exactly. > and running phenix. Not necessarily. This trick should work: bash prompt $ csh csh prompt % source phenix_env csh prompt % bash bash prompt $ Providing a phenix_env.sh is on our todo list. Cheers, Ralf

1 0

Re: [phenixbb] phenixbb Digest, Vol 4, Issue 5
by Petrus H Zwart 12 Mar '06

12 Mar '06

> how to change bash setup ot csh. I guess you can change shell (type csh or so) in a single window for installing, sourcing and running phenix. > In ccp4 there is a file for everything but how to i do for Phenix ! Yes. It is a bit clumsy, I agree. However note that the release you have is still an alpha release (http://en.wikipedia.org/wiki/Development_stage), indicating that not everything is as much in place as one might like it to be. Let us know if you have any (additional) problems. HTH Peter _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

1 0