- phenixbb - phenix-online.org

(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

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Re: [phenixbb] s_annealing within AutoBUILD
by Nicholas Noinaj 15 Jul '06

15 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

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Re: [phenixbb] s_annealing within AutoBUILD
by Ralf W. Grosse-Kunstleve 15 Jul '06

15 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.

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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

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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

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Re: [phenixbb] How to use phenix for SAD data
by Petrus H Zwart 11 Jul '06

11 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

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How to use phenix for SAD data
by pramod＠cdfd.org.in 11 Jul '06

11 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 -

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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

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Problem on Running Phenix
by 崔中利 07 Jul '06

07 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

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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

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