- phenixbb - phenix-online.org

PHENIX 1.4-3 Available
by Paul Adams 23 Dec '08

23 Dec '08

= = = = = ======================================================================== PHENIX 1.4-3 Development Release = = = = = ======================================================================== The PHENIX developers are pleased to announce that the 1.4-3 development version of PHENIX is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ This version of PHENIX includes the following new features: - A new GUI for phenix.xtriage: - To start the GUI version type phenix.xtriage_gui - A new GUI for phenix.refine: - To start the GUI version type phenix.refine_gui - Incorporates a subset of Molprobity validation tools - Documentation for the new GUIs: - See the help menu or button after starting the GUI - Structure refinement (phenix.refine) - Default is to fill missing reflections in map calculations with DFc - Default is to write phase combined maps if experimental phases are used in refinement - Improved capabilities for selection of atoms for occupancy refinement - Xplor maps no longer written by default - Numerous minor bug fixes - Multi-crystal averaging (phenix.multi_crystal_average) - Fast secondary structure building (phenix.find_helices_strands) - Find all ligands in a map (phenix.find_all_ligands) - Minor bug fixes in phenix.elbow and phenix.reel Full documentation is available here: http://www.phenix-online.org/documentation/ There is a PHENIX bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: 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. The development of PHENIX is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the PHENIX Industrial Consortium. = = = = = ======================================================================== PHENIX 1.4-3 Development Release = = = = = ======================================================================== -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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Selection of structure factors for DM
by Graeme Winter 18 Dec '08

18 Dec '08

Hi Folks, If I am using phenix.autosol for my phasing and dm, is there a way I can specify the "native" FP to use for phase extension? What I would like to be able to do is use a named wavelength for this rather than a synthetic data set composed from all input data... I used to do this with resolve by cadding in the chosen columns (F, SIGF) after solve and then telling resolve what columns to use. Would be cute to be able to not do this! Am running from the command line interface. Thanks, Graeme

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Re: [phenixbb] phenixbb Digest, Vol 37, Issue 3
by CNB 17 Dec '08

17 Dec '08

Thanks for the reply. I think I didn't explain myself properly, of course I want to do bss, but we have noticed that previous versions of phenix (1.24 I think) did bss once per macro cycle and now with the newer versions, we get the same plus a final bbs cycle at the end of the whole process -shown in red- Is that final cycle introduced by default in the newer versions? Thanks again. Cesar. REMARK 3_bss: 1.222 0.008 0.075 19.562 0.005 4.107 1.2876e-01 REMARK 3_xyz: 1.021 0.005 0.063 19.049 0.004 4.111 1.0306e-01 REMARK 3_adp: 1.021 0.005 0.063 19.049 0.004 4.111 1.0306e-01 REMARK 3_bss: 1.021 0.005 0.063 19.049 0.004 4.111 1.0306e-01 On Dec 3, 2008, at 9:00 PM, phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://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. Bulk solvent (csantiag(a)cnb.csic.es) > 2. Re: Bulk solvent (junfeng liu) > 3. Re: Bulk solvent (Pavel Afonine) > 4. Re: Bulk solvent (Pavel Afonine) > 5. Re: Question regarding phenix.elbow (Nigel W Moriarty) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 3 Dec 2008 10:15:30 +0100 (CET) > From: csantiag(a)cnb.csic.es > Subject: [phenixbb] Bulk solvent > To: phenixbb(a)phenix-online.org > Message-ID: > <49732.150.244.83.180.1228295730.squirrel(a)webmail.cnb.csic.es> > Content-Type: text/plain;charset=iso-8859-1 > > Hi all, > I'm refining a protein and after running phenix.refine I always get > a bulk > solvent refinement cycle at the end of the process. Is there any > way to > get rid of the last step? > > ---------------------------------------------------------------------- > -- > REMARK stage angl bond chir dihe plan repu > geom_target > REMARK 0 : 1.007 0.027 0.237 18.975 0.004 4.107 > 2.7953e-01 > REMARK 1_bss: 1.007 0.027 0.237 18.975 0.004 4.107 > 2.7953e-01 > REMARK 1_xyz: 1.844 0.015 0.087 19.502 0.005 4.106 > 1.9824e-01 > REMARK 1_adp: 1.844 0.015 0.087 19.502 0.005 4.106 > 1.9824e-01 > REMARK 2_bss: 1.844 0.015 0.087 19.502 0.005 4.106 > 1.9824e-01 > REMARK 2_xyz: 1.222 0.008 0.075 19.562 0.005 4.107 > 1.2876e-01 > REMARK 2_adp: 1.222 0.008 0.075 19.562 0.005 4.107 > 1.2876e-01 > REMARK 3_bss: 1.222 0.008 0.075 19.562 0.005 4.107 > 1.2876e-01 > REMARK 3_xyz: 1.021 0.005 0.063 19.049 0.004 4.111 > 1.0306e-01 > REMARK 3_adp: 1.021 0.005 0.063 19.049 0.004 4.111 > 1.0306e-01 > REMARK 3_bss: 1.021 0.005 0.063 19.049 0.004 4.111 > 1.0306e-01 > REMARK > ---------------------------------------------------------------------- > -- > > > C?sar Santiago > Dept of Macromolecules Structure > Centro Nacional de Biotecnolog?a, CSIC > Campus Cantoblanco > 28049 Madrid > Spain > > csantiag(a)cnb.csic.es > > > > > ------------------------------ > > Message: 2 > Date: Wed, 03 Dec 2008 09:36:30 +0000 > From: junfeng liu <jliu(a)nimr.mrc.ac.uk> > Subject: Re: [phenixbb] Bulk solvent > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <4936531E.5030505(a)nimr.mrc.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Add > > bulk_solvent_and_scale=False > when you run it again. > > > > csantiag(a)cnb.csic.es wrote: >> Hi all, >> I'm refining a protein and after running phenix.refine I always >> get a bulk >> solvent refinement cycle at the end of the process. Is there any >> way to >> get rid of the last step? >> >> --------------------------------------------------------------------- >> --- >> REMARK stage angl bond chir dihe plan repu >> geom_target >> REMARK 0 : 1.007 0.027 0.237 18.975 0.004 4.107 >> 2.7953e-01 >> REMARK 1_bss: 1.007 0.027 0.237 18.975 0.004 4.107 >> 2.7953e-01 >> REMARK 1_xyz: 1.844 0.015 0.087 19.502 0.005 4.106 >> 1.9824e-01 >> REMARK 1_adp: 1.844 0.015 0.087 19.502 0.005 4.106 >> 1.9824e-01 >> REMARK 2_bss: 1.844 0.015 0.087 19.502 0.005 4.106 >> 1.9824e-01 >> REMARK 2_xyz: 1.222 0.008 0.075 19.562 0.005 4.107 >> 1.2876e-01 >> REMARK 2_adp: 1.222 0.008 0.075 19.562 0.005 4.107 >> 1.2876e-01 >> REMARK 3_bss: 1.222 0.008 0.075 19.562 0.005 4.107 >> 1.2876e-01 >> REMARK 3_xyz: 1.021 0.005 0.063 19.049 0.004 4.111 >> 1.0306e-01 >> REMARK 3_adp: 1.021 0.005 0.063 19.049 0.004 4.111 >> 1.0306e-01 >> REMARK 3_bss: 1.021 0.005 0.063 19.049 0.004 4.111 >> 1.0306e-01 >> REMARK >> --------------------------------------------------------------------- >> --- >> >> >> C?sar Santiago >> Dept of Macromolecules Structure >> Centro Nacional de Biotecnolog?a, CSIC >> Campus Cantoblanco >> 28049 Madrid >> Spain >> >> csantiag(a)cnb.csic.es >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> > > > > ------------------------------ > > Message: 3 > Date: Wed, 03 Dec 2008 08:09:57 -0800 > From: Pavel Afonine <pafonine(a)lbl.gov> > Subject: Re: [phenixbb] Bulk solvent > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Cc: csantiag(a)cnb.csic.es > Message-ID: <4936AF55.8010508(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi C?sar, > > this step is important. Bulk solvent modeling is based on mask > calculation and since during refinement of coordinates the atoms shift > the mask gets invalidated. This is why we do a final bulk solvent > correction step at the very last step of refinement just before the > final statistics is reported. So I'm puzzled about why you want to > turn > it off. If it causes any problem, it's much better to find out the > primary reason for it rather than turn bulk solvent correction. Could > you please give more details? > > If you do "main.bulk_solvent_and_scale=false" phenix.refine will > not do > bulk solvent correction and anisotropic scaling at all which is bad. > > Pavel. > > On 12/3/2008 1:15 AM, csantiag(a)cnb.csic.es wrote: >> Hi all, >> I'm refining a protein and after running phenix.refine I always >> get a bulk >> solvent refinement cycle at the end of the process. Is there any >> way to >> get rid of the last step? >> >> --------------------------------------------------------------------- >> --- >> REMARK stage angl bond chir dihe plan repu >> geom_target >> REMARK 0 : 1.007 0.027 0.237 18.975 0.004 4.107 >> 2.7953e-01 >> REMARK 1_bss: 1.007 0.027 0.237 18.975 0.004 4.107 >> 2.7953e-01 >> REMARK 1_xyz: 1.844 0.015 0.087 19.502 0.005 4.106 >> 1.9824e-01 >> REMARK 1_adp: 1.844 0.015 0.087 19.502 0.005 4.106 >> 1.9824e-01 >> REMARK 2_bss: 1.844 0.015 0.087 19.502 0.005 4.106 >> 1.9824e-01 >> REMARK 2_xyz: 1.222 0.008 0.075 19.562 0.005 4.107 >> 1.2876e-01 >> REMARK 2_adp: 1.222 0.008 0.075 19.562 0.005 4.107 >> 1.2876e-01 >> REMARK 3_bss: 1.222 0.008 0.075 19.562 0.005 4.107 >> 1.2876e-01 >> REMARK 3_xyz: 1.021 0.005 0.063 19.049 0.004 4.111 >> 1.0306e-01 >> REMARK 3_adp: 1.021 0.005 0.063 19.049 0.004 4.111 >> 1.0306e-01 >> REMARK 3_bss: 1.021 0.005 0.063 19.049 0.004 4.111 >> 1.0306e-01 >> REMARK >> --------------------------------------------------------------------- >> --- >> >> >> C?sar Santiago >> Dept of Macromolecules Structure >> Centro Nacional de Biotecnolog?a, CSIC >> Campus Cantoblanco >> 28049 Madrid >> Spain >> >> csantiag(a)cnb.csic.es >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > > ------------------------------ > > Message: 4 > Date: Wed, 03 Dec 2008 08:13:21 -0800 > From: Pavel Afonine <pafonine(a)lbl.gov> > Subject: Re: [phenixbb] Bulk solvent > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Message-ID: <4936B021.7010401(a)lbl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Yes, this will turn bulk solvent correction and anisotropic scaling > off > completely. In some cases it may result in R-factors increase by > ~5% or > similar. So it may only make sense in exotic cases or if you do > numerical experiments (simulated data etc..). > > Pavel. > > > On 12/3/2008 1:36 AM, junfeng liu wrote: >> Add >> >> bulk_solvent_and_scale=False >> when you run it again. >> >> >> >> csantiag(a)cnb.csic.es wrote: >> >>> Hi all, >>> I'm refining a protein and after running phenix.refine I always >>> get a bulk >>> solvent refinement cycle at the end of the process. Is there any >>> way to >>> get rid of the last step? >>> >>> -------------------------------------------------------------------- >>> ---- >>> REMARK stage angl bond chir dihe plan repu >>> geom_target >>> REMARK 0 : 1.007 0.027 0.237 18.975 0.004 4.107 >>> 2.7953e-01 >>> REMARK 1_bss: 1.007 0.027 0.237 18.975 0.004 4.107 >>> 2.7953e-01 >>> REMARK 1_xyz: 1.844 0.015 0.087 19.502 0.005 4.106 >>> 1.9824e-01 >>> REMARK 1_adp: 1.844 0.015 0.087 19.502 0.005 4.106 >>> 1.9824e-01 >>> REMARK 2_bss: 1.844 0.015 0.087 19.502 0.005 4.106 >>> 1.9824e-01 >>> REMARK 2_xyz: 1.222 0.008 0.075 19.562 0.005 4.107 >>> 1.2876e-01 >>> REMARK 2_adp: 1.222 0.008 0.075 19.562 0.005 4.107 >>> 1.2876e-01 >>> REMARK 3_bss: 1.222 0.008 0.075 19.562 0.005 4.107 >>> 1.2876e-01 >>> REMARK 3_xyz: 1.021 0.005 0.063 19.049 0.004 4.111 >>> 1.0306e-01 >>> REMARK 3_adp: 1.021 0.005 0.063 19.049 0.004 4.111 >>> 1.0306e-01 >>> REMARK 3_bss: 1.021 0.005 0.063 19.049 0.004 4.111 >>> 1.0306e-01 >>> REMARK >>> -------------------------------------------------------------------- >>> ---- >>> >>> >>> C?sar Santiago >>> Dept of Macromolecules Structure >>> Centro Nacional de Biotecnolog?a, CSIC >>> Campus Cantoblanco >>> 28049 Madrid >>> Spain >>> >>> csantiag(a)cnb.csic.es >>> >>> >>> _______________________________________________ >>> 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 >> >

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B-group and TLS
by Engin Ozkan 16 Dec '08

16 Dec '08

Dear phenixbb people, I am performing group ADP refinement and TLS at the same time. At the end, the total B factors in the pdb are not identical within residue groups. ATOM 7 N ILE A 11 23.863 6.894 77.827 1.00151.81 A N ANISOU 7 N ILE A 11 20044 20245 17393 -796 -2448 -568 A N ATOM 8 CA ILE A 11 23.647 6.312 76.502 1.00149.93 A C ANISOU 8 CA ILE A 11 19407 19827 17732 -699 -2577 -541 A C ATOM 9 CB ILE A 11 24.451 7.060 75.423 1.00142.17 A C ANISOU 9 CB ILE A 11 18258 18757 17003 -502 -2834 -817 A C ATOM 10 CG2 ILE A 11 24.819 6.135 74.260 1.00140.21 A C ANISOU 10 CG2 ILE A 11 17760 18301 17213 -445 -3136 -730 A C ATOM 11 CG1 ILE A 11 23.648 8.266 74.929 1.00141.20 A C ANISOU 11 CG1 ILE A 11 17949 18698 17002 -369 -2502 -1103 A C ATOM 12 CD1 ILE A 11 22.184 7.945 74.630 1.00147.23 A C ANISOU 12 CD1 ILE A 11 18421 19495 18025 -392 -2156 -1014 A C ATOM 13 C ILE A 11 24.000 4.831 76.450 1.00152.71 A C ANISOU 13 C ILE A 11 19772 20013 18238 -798 -2860 -201 A C ATOM 14 O ILE A 11 24.895 4.377 77.158 1.00153.29 A O ANISOU 14 O ILE A 11 20114 20074 18055 -857 -3135 -9 A O I would like to know if the refinement was truly grouped B-factor refinement - I am suspecting the residual B-factors might be grouped, but I haven't checked for that. Could anyone, maybe Pavel, confirm that is the case? Is there anyplace in the log files I could see the number of B groups? Thanks, Engin

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Re: [phenixbb] Completeness issue by phenix
by Young-Jin Cho 16 Dec '08

16 Dec '08

Thanks Ralf, You were right. I found that my .log file has Anomalous flag:True. As it was pointed out, my mtz file was came from ccp4 where it uses anomalous data by default. Another small wondering is about differently automatic(?) resolution pick up: my refmac assigned resolution range between 1.48 and 54.23 whereas my phenix.refine set it between 1.363 and 31.041 by default. Also while the refmac provides both entire and high resolution bin completeness, the phenix only gives a whole completeness. Is there any way I can investigate high resolution bin completeness? and why I have different resolution ranges by default without specifically assigning them? Thanks again. YoungJin ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" <rwgk(a)cci.lbl.gov> To: phenixbb(a)phenix-online.org Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Completeness issue by phenix Hi YoungJin, I suspect phenix.refine decided your mtz file contains anomalous data when you actually have non-anomalous data. Could you look in the phenix.refine output for something like this: ================================== X-ray data ================================= F-obs: 1yjp.mtz:FOBS_X,SIGFOBS_X R-free flags: 1yjp.mtz:R-free-flags Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X Observation type: xray.amplitude Type of data: double, size=495 Type of sigmas: double, size=495 Number of Miller indices: 495 Anomalous flag: False ^^^^^ in particular here If you see "Anomalous flag: True" try adding this to the phenix.refine command line: xray_data.force_anomalous_flag_to_be_equal_to=False Let me know if this doesn't help. If it does help, I'd be interested to know how the .mtz file was generated. Ralf _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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Re: [phenixbb] Completeness issue by phenix
by Ralf W. Grosse-Kunstleve 15 Dec '08

15 Dec '08

Hi Rupert, Thank you very much for the files! I found a simple, universal trick to "do the right thing", not just in phenix.refine. This will be in future releases. Ralf

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Completeness issue by phenix
by Young-Jin Cho 15 Dec '08

15 Dec '08

Hi, I was happy for using phenix but am struggling with a strange result on completeness calculation. One typical data set I used kept showing low completeness, so I used the same mtz, and pdb file on Refmac: it turned out has more than 98% whereas phenix.refine gave me about 46% completeness. I have slightly lower value of R but higher Rfree from phenix calculation without adding H atoms. I don't know if this is a bug or a problem on my data set (hopefully not). thanks in advance, YoungJin

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phenix GUI takes longer time to comeup
by shivesh kumar 15 Dec '08

15 Dec '08

Dear all The GUI of phenix installed in Fedora 8 takes longer time, sometimes 30mins. Can anyone help in this regard, what is the problem and how it can be sorted out? Thanx in advance Shivesh

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Re: [phenixbb] individual anisotropic adps
by Pavel Afonine 13 Dec '08

13 Dec '08

Currently phenix.refine does not support refinement of individual anisotropic ADP and TLS for the same set of atoms (see my previous email). However, in phenix.refine you can refine TLS and individual anisotropic ADP for non-overlapping set of atoms. Pavel. On 12/11/2008 8:34 AM, gerwald jogl wrote: > Thanks, that's roughly what I thought. How about tls and individual > anisotropic together? same strategy, just observe Rfree?

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individual anisotropic adps
by gerwald jogl 11 Dec '08

11 Dec '08

Hi All, I was wondering if there is information/recommendations out there for the resolution required to refine individual anisotropic adps. I think the recommendation for shelx is at least 1.5 A resolution. In addition, is phenix set up and would it make sense to combine tls with individiual anisotropic adps? All comments welcome, Gerwald

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