December 2008 - phenixbb - phenix-online.org

rmsd: phenix vs refmac
by Frank von Delft 26 Jan '09

26 Jan '09

Hi I thought that a while ago, I read somewhere that rmsd(bonds) had not been calculated the same way in phenix as in refmac. I believe it was in connection with automated weights, and that rmsd(bonds) always much lower in phenix. I understood too that this had been adjusted since to match refmac. But we're still seeing some much lower rmsd(bond) from phenix: in particular, when we take a refmac model and plug it straight into phenix, the rmsd for cycle zero is already much lower than what it was at the end of refmac. Could someone enlighten...? (Yup, latest version of phenix.) Thanks! phx

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Unmasking cavities
by Frank von Delft 24 Jan '09

24 Jan '09

Hi After being through phenix.refine, I see in my hydrophobic core a big space (a few atoms wide) that is filled with strong negative difference density. I suspect the culprit is the bulk solvent mask, which is defined too tightly. The online manual mentions three parameters, but not what they do. solvent_radius, shrink_truncation_radius, grid_step_factor What *exactly* do they do? (I thought I'd elicit a contribution for the online docs this way :) Cheers phx

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fixing a partial solution of mol. rep.
by chern 07 Jan '09

07 Jan '09

I am doing a molecular replacement. There are two types of protein molecules in the crystal. One type is forming a hexameric core; there are 6 molecules of the second type that I need to locate. I found a solution for the hexameric core, but the other 6 molecules are difficult to find. 1. Can I fix the solution for the core, so that I don't have to find it every time. The other inconvenience with that is that the origine is different for every new run. If I fix the hexamer, then I fix the origine. It's important to me to compare different runs of MR. 2. Some of the six other molecules that MR finds are not the closest to the core. How can I request to output the closest molecules? Maia

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Error
by Miles Pufall 28 Dec '08

28 Dec '08

Hi - It appears there was a problem with the NCS flag being on, and when I took it off I received this error. Let me know if you'd like data to recreate this. Cheers - Miles RuntimeError : OpenGL: invalid operation Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 188, in run self.check_params_and_run() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 229, in check_params_and_run self.model.add_hydrogens() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Model.py", line 369, in add_hydrogens self.update_from_interface() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Model.py", line 181, in update_from_interface self.update_viewer() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Model.py", line 317, in update_viewer self .viewer_frame.glview.update_structure_from_files(self.get_all_files()) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 166, in update_structure_from_files self.update_structure(pdb_hierarchy, atomic_bonds, redraw=True) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 180, in update_structure self.OnUpdate(recenter=True) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 208, in OnUpdate self.update_view(True, True) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 566, in update_view self.OnRedraw() File "/usr/local/phenix-1.4-3/gltbx/wx_viewer.py", line 473, in OnRedraw self.OnRedrawGL(event) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 118, in OnRedrawGL wx_viewer.wxGLWindow.OnRedrawGL(self, event) File "/usr/local/phenix-1.4-3/gltbx/wx_viewer.py", line 476, in OnRedrawGL gltbx.util.handle_error() RuntimeError: OpenGL: invalid operation Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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PHENIX 1.4-3 Available
by Paul Adams 24 Dec '08

24 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 18 Dec '08

18 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 17 Dec '08

17 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 17 Dec '08

17 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 16 Dec '08

16 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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