- phenixbb - phenix-online.org

Re: [phenixbb] questions / TLS+NCS bug
by Pavel Afonine 14 Dec '06

14 Dec '06

Hi Jianghai, Thanks for the .log file ! I looked at it and now I think I now what's the problem: this is the bug in phenix.refine that we will fix for the next release. The bug arises when you try to refine using TLS and NCS at once. Sorry for this. The possible solution is to split your refinement into 2 parts: 1) First, refine coordinates and isotropic B-factors. Use NCS restraints. DO NOT refine TLS. 2) At the end, as the final tune up, refine ONLY isotropic B-factors + TLS and do not refine coordinates. For this run, please REMOVE all NCS information (NCS selections) from the command file. This refinement run should be the final one. Once again, sorry for the inconvenience. This will be fixed in the next release of CCI APPS and PHENIX. Once this fixed, you will be able to run everything in "one go" and in any combination. Please let me know if what I suggested helped you. Any further questions are welcome! Cheers, Pavel. Jianghai Zhu wrote: > Here is the log file. Thanks. > > Jianghai > > = > ------------------------------------------------------------------------ > > > > On Dec 14, 2006, at 12:50 PM, Pavel Afonine wrote: > >> Hi Jianghai, >> >> could you please send us .log file from your refinement run, so we >> can analyze what's going on. >> >> In general, "bad" B-factors can be: >> - misplaced model; >> - inadequate TLS model (= domains chosen for TLS do not correspond to >> the reality). >> >> If you are using like 2 months old or older version of phenix.refine, >> you may want to get the latest CCI APPS since we made lots of >> improvements. Just goto http://www.phenix-online.org/download/cci_apps/ >> >> Pavel. >> >> >> Jianghai Zhu wrote: >>> The resolution is 2.5 A. The wilson B is about 50. I know B factor >>> of the backbone is lower than that of the sidechian. But a B factor >>> like 4 is definitely wrong. >>> >>> Jianghai >>> >>> >>> On Dec 14, 2006, at 12:11 PM, Peter Zwart wrote: >>> >>>> >>>>>> 4) The refinement (TLS + ML + B individual) went through, I got >>>>>> reasonable R, Rfree, rmsdBOND, rmsdANGLE. But the B factors are >>>>>> pretty low. The B factor of the backbone is much lower than the >>>>>> side >>>>>> chain, some have numbers like 4. Some metal atoms also have B >>>>>> factors around 4. What did I do wrong? >>>> >>>> What is the resolution of your data? >>>> >>>> Backbone B-s usually are lower than the main chain. >>>> >>>> What is the Wilson B value reported by phenix.refine? >>>> You could re-refine and randomize all B-values and see what happens (I >>>> have to get back to you to to get the exact command for this). >>>> Maybe it >>>> is useful to obtain a copy of the latest verison of phenix.refine by >>>> downloading cci_apps from our server http://www.phenix-online.org. >>>> >>>> >>>> If your B-values still come out lowish, try growing crystals that >>>> do not >>>> diffract very well, that usually does the trick. >>>> >>>> HTH >>>> >>>> Peter >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org <mailto:[email protected]> >>>> 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 <mailto:[email protected]> >> http://www.phenix-online.org/mailman/listinfo/phenixbb > > =

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Re: [phenixbb] questions
by Ralf W. Grosse-Kunstleve 14 Dec '06

14 Dec '06

> 3) When I ran phenix.refine, I found the following message in the log. > > Number of residues, atoms: 32, 418 > Unusual residues: {'NAG': 22, 'MAN': 10} > Classifications: {'undetermined': 32} "Unusual" means "not peptide, rna/dna, or water". It is just for information. If phenix.refine cannot find matching CIF restraint definitions, it will report "Unknown residues". Ralf

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NCS in phenix.refine
by Alessandro S. Nascimento 13 Dec '06

13 Dec '06

Hi all, I've searched in phenix manuals but I didn't find how to deal with ncs in parameter file. Also, how to prepare simulated annealing keeping ncs restraints? Is it already possible in 1.24b version? Any idea? thanks, - alessandro

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Maybe a bug?
by Zhongli Cui 22 Nov '06

22 Nov '06

Phenix is a quite useful suite in solving protein structure. But I met a problem during running phenix1.24.1b on a suse 10.1 environment. When I try to load pdb file from the window, the phenix GUI will close automatically. But it runs OK, if I input the file name manually into the window.

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refining a twin
by Bryan W. Lepore 21 Nov '06

21 Nov '06

i see there are map utilities for twinned data. but before i go try refinement of a twin - will phenix.refine refine against twinned data? if so, is alpha determined each time, thus, alpha is not specified in the .def? -bryan

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HA clusters
by Morten Grøftehauge 13 Nov '06

13 Nov '06

Hi, This is probably a stupid question but how do I tell AutoSol to look for a heavy-atom cluster rather than individual atoms? Or should I just find the cluster as a superatom in CNS and input the refined co-ordinates? Thanks, -- Morten K Grøftehauge PhD student Department of Molecular Biology Gustav Wieds Vej 10 C 8000 Aarhus C - Denmark Phone: +45 89 42 50 10 Fax: +45 86 12 31 78 www.bioxray.dk

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fixing atoms during refinement
by Gregers Andersen 02 Nov '06

02 Nov '06

Is there anyway through selection to fix selected atoms during minimisation/sim annealing in phenix.refine? Gregers Rom Andersen Associate Professor, Ph.D. Dep. Molecular Biology Gustav Wiedsvej 10C DK8000 Aarhus C Denmark phone +4589425024 fax +4586123178 <http://www.bioxray.dk/research_gra_uk.php> http://www.bioxray.dk/research_gra_uk.php Please notice new email: <mailto:[email protected]> gra(a)mb.au.dk

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a few questions
by Jianghai Zhu 23 Oct '06

23 Oct '06

Hi All, I have a few questions about phenix.refine and I couldn't find the answer in the manual. 1) How to generate the ligand library in phenix.refine? 2) Can phenix.refine calculate an OMIT COMPOSITE map? 3) When I used ML as the target, I couldn't find the output of LLG or similar number in the log file. How do I know the refinement is converged? 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: 618-278-3232 +++++++++++++++++++++++++++++++

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a few questions
by Jianghai Zhu 22 Oct '06

22 Oct '06

Hi All, I have a few questions about phenix.refine and I couldn't find the answer in the manual. 1) How to generate the ligand library in phenix.refine? 2) Can phenix.refine calculate an OMIT COMPOSITE map? 3) When I used ML as the target, I couldn't find the output of LLG or similar number in the log file. How do I know the refinement is converged? 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: 618-278-3232 +++++++++++++++++++++++++++++++

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Phenix 1.24 and Fedora Core 5_64
by Nicholas Noinaj 09 Oct '06

09 Oct '06

Hi, I have loaded PHenix 1.24 onto a system with Fedora Core 5 (ix86_64). THe computer has an AMD X2_64 4400+ processor, 2 GB RAM, 3X120GB Sata HDs, ASUS A8N-Sli Premium Mobo, and an Nvidia 7600 GT graphics card. When I install PHenix, everything seems to load okay, except it seems to take a bit longer to install than with RHEL3 did, stalling for bit on one of the modules (sorry, can't remember which one exactly). Then after a while, the installation completes without any errors and I setup the environment as instructed for /bin/bash. I then type [phenix] to start the program, but again nothing happens for a very long time (30 minutes or more), and then the Phenix interface finally loads. But then, everything is very sluggish and takes a very long time to load or even stops responding (setup/parameter windows in particular). I have installed Phenix 1.24 on RHEL3 and not experienced any of these problems, so I am a bit clueless. FUrther, I am a Linux 'newbie' and this was my first time installing Fedora Core 5 (64), so it is possible that i haven't installed everything that Phenix needs, yet I did not experience any problems at all with the FC5 installation, ran smoothly. If you have any suggestions or insights as to what my problem or mistake may be, I thank you in advance for your feedback and assistance. I am eager to get Phenix purring away on my latest PC. Cheers, Nick the environment as instructed for /bin/bash. I then type [phenix] to start the program, but again nothing happens for a very long time (30 minutes or more), and then the Phenix interface finally loads. But then, everything is very sluggish and takes a very long time to load or even stops responding (setup/parameter windows in particular). I have installed Phenix 1.24 on RHEL3 and not experienced any of these problems, so I am a bit clue ________________________________________ Nicholas Noinaj University of Kentucky College of Medicine Department of Molecular and Cellular Biochemistry The Center for Structural Biology Biomedical Biological Sciences Research Building, Rm 236 741 S. Limestone Lexington, Ky 40536 Lab: 859-323-8183 Cell: 859-893-4789 Home: 859-228-0978 noinaj(a)uky.edu noinaj.com

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Re: [phenixbb] Solvent in Auto_Build
by Thomas C. Terwilliger 10 Sep '06

10 Sep '06

Hi Jeff, I think if you edit the file to replace 'ATOM ' with 'HETATM' for all the HOH records then it should work. Please let me know if it doesn't! -Tom T > Dear Dr. Adams, and/or other Phenix experts, > > > > I have done water-picking in CNS and some refinement in Refmac-5 in > ccp4 and subsequent manual adjustments of waters in Coot and O. I have > discovered that CNS seems to like the format 'OH2 TIP' for listing waters, > whereas refmac only likes HOH. When I then run Auto_Build in the Phenix > GUI, I get the following error message: > > > > Input failed > > Sorry, the PDB file /path/filename.pdb has an incomplete residue (or > conformer/residue combination) in conformer ' ' chain S residue HOH 733 > because the conformer is missing the following main chain atoms: [ 'N', > 'CA', 'C' ]. > > > > The first water in my pdb file is indeed the one in question above. > Apparently Phenix is thinking that this water should be a protein residue > instead of solvent. Can anyone help me with this and tell me what I need > to > edit in the pdb file so that Phenix recognizes it as solvent instead of > protein, or do I need to delete all waters and repick them in Phenix. I > have tried changing the segid to from A to S with no success. > > > > Many Thanks, > > > > Jeff B. > > > > > > > > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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Solvent in Auto_Build
by Jeff Bush 10 Sep '06

10 Sep '06

Dear Dr. Adams, and/or other Phenix experts, I have done water-picking in CNS and some refinement in Refmac-5 in ccp4 and subsequent manual adjustments of waters in Coot and O. I have discovered that CNS seems to like the format 'OH2 TIP' for listing waters, whereas refmac only likes HOH. When I then run Auto_Build in the Phenix GUI, I get the following error message: Input failed Sorry, the PDB file /path/filename.pdb has an incomplete residue (or conformer/residue combination) in conformer ' ' chain S residue HOH 733 because the conformer is missing the following main chain atoms: [ 'N', 'CA', 'C' ]. The first water in my pdb file is indeed the one in question above. Apparently Phenix is thinking that this water should be a protein residue instead of solvent. Can anyone help me with this and tell me what I need to edit in the pdb file so that Phenix recognizes it as solvent instead of protein, or do I need to delete all waters and repick them in Phenix. I have tried changing the segid to from A to S with no success. Many Thanks, Jeff B.

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Re: [phenixbb] phenixbb Digest, Vol 10, Issue 1
by Pramod Kumar JRF 05 Sep '06

05 Sep '06

Hi I am running structure solution strategy- solve MAD and 'top' is also doesnot shows that anything is running. and also 'Task' is also never appered on the taskbar alongwith wizards and strategies. 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 On Fri, 1 Sep 2006 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://www.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. Strategies is not working on IRIX (Pramod Kumar JRF) > 2. Re: Strategies is not working on IRIX (Paul Adams) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Sep 2006 08:51:24 -0700 > From: Pramod Kumar JRF <pramod(a)cdfd.org.in> > Subject: [phenixbb] Strategies is not working on IRIX > To: phenixbb(a)phenix-online.org > Message-ID: > <Pine.SGI.4.44.0609010841320.231393-100000(a)www.cdfd.org.in> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi > I have installed the IRIX version of the phexinx1.24b.I am able to run > the wizards on my sgi but not strategies. Even after several hours its not > turning green,which is an indication that its not running.what could be > the problem? > > thanks in advance > > With regards > Pramod Kumar, > c/o Dr. Shekhar C. Mande > Lab of structural biology > Center for DNA Fingerprinting and Diagnostics > ECIL Road, Nacharam, > Hyderabad-500076 > India > > > > > > > ------------------------------ > > Message: 2 > Date: Fri, 01 Sep 2006 08:58:41 -0700 > From: Paul Adams <PDAdams(a)lbl.gov> > Subject: Re: [phenixbb] Strategies is not working on IRIX > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <44F858B1.3000507(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > which strategy are you trying to run. Does 'top' show anything running? > > Cheers, > Paul > > Pramod Kumar JRF wrote: > > Hi > > I have installed the IRIX version of the phexinx1.24b.I am able to run > > the wizards on my sgi but not strategies. Even after several hours its not > > turning green,which is an indication that its not running.what could be > > the problem? > > > > thanks in advance > > > > With regards > > Pramod Kumar, > > c/o Dr. Shekhar C. Mande > > Lab of structural biology > > Center for DNA Fingerprinting and Diagnostics > > ECIL Road, Nacharam, > > Hyderabad-500076 > > India > > > > > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > -- > Paul Adams > Senior Staff Scientist, Physical Biosciences Division > Head, Berkeley Center for Structural Biology > Deputy Principal Investigator, Berkeley Structural Genomics Center > > Building 64, Room 248 > Tel: 510-486-4225, Fax: 510-486-5909 > http://cci.lbl.gov/ > > Lawrence Berkeley Laboratory > 1 Cyclotron Road > BLDG 64R0121 > Berkeley, CA 94720, USA. > -- > > > ------------------------------ > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > End of phenixbb Digest, Vol 10, Issue 1 > *************************************** >

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Re: [phenixbb] Phenix 1.24.1 update/reinstall
by Petrus H Zwart 01 Sep '06

01 Sep '06

No way to update, just reinstall from scratch. Remove the sourcing of the phenix_env file from the .cshrc file (or so) and replace iot with what the phenix installer tells you. You can leave the old phenix sources sitting on your disc for senstimental reasons, or just remove it. A small tip, source your phenix distribution after you source ccp4. This will ensure that the most upto date version of various cctbx command line utilities will be used (otherwise you might have to call mmtbx.xtriage_1.24.1b instead of mmtbx.xtriage) HTH Peter Hi, i have Phenix 1.1 installed on a Linux workstation and would like to update it to Phenix 1.24.1. Is there a way to just update the old version or do I need to uninstall Phenix 1.1 and then install Phenix 1.24.1? If I need to uninstall Phenix 1.1, what is the best approach to accomplish this (sorry, Linux newbie)? Thanks in advance for all your feedback! 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 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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Phenix 1.24.1 update/reinstall
by Noinaj 01 Sep '06

01 Sep '06

Hi, i have Phenix 1.1 installed on a Linux workstation and would like to update it to Phenix 1.24.1. Is there a way to just update the old version or do I need to uninstall Phenix 1.1 and then install Phenix 1.24.1? If I need to uninstall Phenix 1.1, what is the best approach to accomplish this (sorry, Linux newbie)? Thanks in advance for all your feedback! 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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Strategies is not working on IRIX
by Pramod Kumar JRF 01 Sep '06

01 Sep '06

Hi I have installed the IRIX version of the phexinx1.24b.I am able to run the wizards on my sgi but not strategies. Even after several hours its not turning green,which is an indication that its not running.what could be the problem? thanks in advance With regards Pramod Kumar, c/o Dr. Shekhar C. Mande Lab of structural biology Center for DNA Fingerprinting and Diagnostics ECIL Road, Nacharam, Hyderabad-500076 India

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Re: [phenixbb] phase extension through phenix
by Tom Terwilliger 11 Aug '06

11 Aug '06

Hi Pramod, >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? In the version you have, unfortunately the AutoSol keywords res_phase and resolution do almost the same thing, so you cannot do what you are asking for. This is fixed for the next version. An update patch will be available shortly to do it as well. I'm sorry for the problem! -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

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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

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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

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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

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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 +++++++++++++++++++++++++++++++

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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

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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

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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-----

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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 >

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(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 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

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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.

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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 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

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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 -

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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 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

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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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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

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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

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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

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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. | ==========================================================

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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

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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/ -----------------------------------------------------

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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

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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

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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

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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

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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

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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

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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

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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 >

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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

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