- phenixbb - phenix-online.org

SAD and autosol
by Tom Terwilliger 11 Aug '06

11 Aug '06

Hi Pramod, >Hi all I am new user of the phenix. I am using autosol for the SAD data of >the 3.5 Ang of resolution data of spacegroup P42212. After running autosol >with all inputs , during Hyss autosol is not able to move forard with >display of followimg information: > > >Top solution : # 2 Dataset #1 >score: -1000 Fom: 0.19 sites:1 > > >Failed to carry out Autosol_score_ha_solutions: >list index out of range >STEP: Autosol_score_ha_solutions I'm sorry about this problem. I haven't seen it before, and I would like to track it down. I assume you are using version 1.24.1b, is that correct? If you would like to send me the data for this (as a .tar or .tgz file, renamed to ".txt") I will try it out on my computer. 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://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.tbgenomics.org

1 0

phase extension through phenix
by Pramod Kumar JRF 11 Aug '06

11 Aug '06

Hi all I have one more question. Is any way in phenix GUI through which i can do phasing to lowere resolution, further phase extension to higher resolution? Becouse, my SAD data with single SeMet in whole protein of 3.5 Ang which have somewhat better phases and FOM at 5.0 ang resolution than 3.5 Ang resolution. Is it possible through phenix? If anybody have any one can help me? Thanks in advance. Pramod Kumar, c/o Dr. Shekhar C. Mande Lab of structural biology Center for DNA Fingerprinting and Diagnostics ECIL Road, Nacharam, Hyderabad-500076 India

1 0

SAD and autosol
by Pramod Kumar JRF 11 Aug '06

11 Aug '06

Hi all I am new user of the phenix. I am using autosol for the SAD data of the 3.5 Ang of resolution data of spacegroup P42212. After running autosol with all inputs , during Hyss autosol is not able to move forard with display of followimg information: Top solution : # 2 Dataset #1 score: -1000 Fom: 0.19 sites:1 Failed to carry out Autosol_score_ha_solutions: list index out of range STEP: Autosol_score_ha_solutions Thanks in advance Pramod Kumar, c/o Dr. Shekhar C. Mande Lab of structural biology Center for DNA Fingerprinting and Diagnostics ECIL Road, Nacharam, Hyderabad-500076 India

1 0

a few questions
by Jianghai Zhu 06 Aug '06

06 Aug '06

Hi all, I have a structure refined to 2.5 A. After simulated annealing (start temp = 5000, cool rate = 25, final temp = 100, include TLS refinement and NCS restraint), my R and Rfree are 24.6% and 28.7% respectively. I then turned off the SA in the generated def file and carried on the combined refinement. My R and Rfree went up to 25% and 29.2% respectively. Why did the Rfree go up after refinement? In the remarks of the output pdb file, I have one line, "REMARK twinned : True". What does this mean? The RMSD of bonds and angles after either SA or combined refinement are about 0.006 and 0.851 respectively. Don't you guys think the geometry restraints are too tight? How do I change the weight in PHENIX? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3030 +++++++++++++++++++++++++++++++

3 4

Autobuild peptide?
by ckielkop 02 Aug '06

02 Aug '06

Hi, We have a molecular replacement RNA structure with a bound peptide. I'd like phenix autobuild the peptide, because only a portion of it is bound and we'd like an unbiased, silicon opinion about what that portion is. It's not clear to me how to proceed with this in phenix- we have a beautiful electron density map from CNS, coordinates for the RNA portion, and peptide sequence. Thanks for any guidance! -- Clara L. Kielkopf Assistant Professor Biochemistry and Molecular Biology Johns Hopkins University Rm. W8708 BSPH 615 N. Wolfe St. Baltimore, MD 21205 Ph. 443-287-4546

3 2

Build problems: 1.24.1b on SLES9
by Chris Richardson 01 Aug '06

01 Aug '06

Dear all, I've just been trying to install 1.24.1 beta on a new server running SuSE Linux Enterprise Server 9. The machine's a dual Xeon, so I've been using the 64-bit linux 2.6 build. I'm invoking install with ./install --prefix=/common/app/phenix-1.24.1b Installation fails with the message configuring PHENIX components Error configuring: see /common/app/phenix-installer-1.24.1b/ build-binary/intel-linux-2.6-x86_64/zaltu/log/binary.log for details Looking at the log file, the last few lines are ./iotbx/iotbx/shelx/from_ins.py ./iotbx/iotbx/shelx/write_ins.py ./ccp4io_502_cci/ ./ccp4io_502_cci/lib/ ./ccp4io_502_cci/lib/src/ ./ccp4io_502_cci/lib/data/ ./ccp4io_502_cci/lib/data/symop.lib ./ccp4io_502_cci/CCI_DIFFS python: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory SLES v9 uses libstdc++.so.5. Python works fine on this machine and is linked to libstdc++.so.5. I assume (probably incorrectly) that the error comes from some component of Phenix that is linked to the later version of the library. Does anybody have handy hints for installation on SLES? I would try it with SLES v10, but that would conflict with other packages we have running on that machine. TIA, Chris -- Dr Chris Richardson - sysadmin, Structural Biology Section, icr.ac.uk

1 0

Problems running demo
by Miguel Ortiz Lombardia 31 Jul '06

31 Jul '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, Sorry if this kind of problems have been posted before, I tried unsuccessfully to find a relevant FAQ. I'm new to Phenix, so I thought it would be a good idea to run the GUI demo first. I installed, set up the programs and copied the data in a directory and did as instructed in the demonstration sequence page. I find two problems: 1. When I call the GUI I don't see the Tasks tab (well, perhaps not a problem, just a misunderstanding) 2. After I load the AutoSol wizard and press "Continue" the wizard doesn't turn to green. Instead, it remains blue and get this message in the console: (...) SUMMARY Input files dataset #1 peak.sca Creating new Data Storage /home/miguel/tests/phenix_demo/PDS/AutoSol.1 Traceback (most recent call last): File "/usr/local/phenix-1.24.1b/phenix/phenix/pds_server/ProcessMaster.py", line 269, in ? run() File "/usr/local/phenix-1.24.1b/phenix/phenix/pds_server/ProcessMaster.py", line 193, in run tasklist = strategyDataStorage.getObject(ProcessKey) File "/usr/local/phenix-1.24.1b/phenix/phenix/server/PDSClient.py", line 146, in getObject return self.loader(pickle_string) File "/usr/local/phenix-1.24.1b/phenix/phenix/server/PDSClient.py", line 27, in loader self.loader(pickle_string) File "/usr/local/phenix-1.24.1b/phenix/phenix/server/PDSClient.py", line 17, in loader return cPickle.loads(pickle_string) ValueError: could not convert string to float Any ideas of what may be wrong? Cheers, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: molatwork(a)yahoo.es www: http://www.ysbl.york.ac.uk/~mol/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (GNU/Linux) iD8DBQFEzgoeF6oOrDvhbQIRAn6SAJ4zmtiWyYJhmB7hdJeEGUp3kr0MtACfYffg ZvyFTX9ExvysvTOav35k0pg= =nS7A -----END PGP SIGNATURE-----

2 4

Re: [phenixbb] (no subject)
by Petrus H Zwart 28 Jul '06

28 Jul '06

The easiest way is to run the AutoBuild wizard. It will do modelbuilding and density modification for you. HTH Peter Zwart ----- Original Message ----- From: sroy(a)mbu.iisc.ernet.in Date: Friday, July 28, 2006 4:57 am Subject: [phenixbb] (no subject) > Hi all, > I am first time using phenix GUI. I have a moleculat > replacementsolution. PDB file contain a polyala model. I want to > do density > modification using resolve in phenix. how to do? > please help > sidhu > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

1 0

(no subject)
by sroy＠mbu.iisc.ernet.in 28 Jul '06

28 Jul '06

Hi all, I am first time using phenix GUI. I have a moleculat replacement solution. PDB file contain a polyala model. I want to do density modification using resolve in phenix. how to do? please help sidhu

1 0

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