- 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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Keeping the same origin
by Mo Wong 11 Dec '08

11 Dec '08

Hi all, I would like to compare maps from different phasing runs, so it would make my life much easier if I could keep the same origin. I recall this could be done in solve/resolve, but can't seem to find it mentioned in the phenix documentation. Any suggestions? Thanks!

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resolution bins
by Daniele de Sanctis 10 Dec '08

10 Dec '08

Hi, I was wondering how phenix.refine decide the number of resolution bins in which it shows the refinement statistics (R-free, phase error...). In the case I'm working on it prints out only three resolution bins. Thanks d -- Daniele de Sanctis, PhD Macromolecular Crystallography Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

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Question regarding phenix.elbow
by Young-Jin Cho 03 Dec '08

03 Dec '08

Hi I would like to know how I can add H atoms to my ligand, ADP in the protein complex. I was trying to add H atoms to one of my ligand, ADP. When I types "phenix.elbow --final-geometry=test10bcoot_h_refine_001.pdb --residue=ADP --output=model_h", it went on but failed with the following error message: Traceback (most recent call last): File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1201, in <module> run() File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1108, in run molecule = post_process(molecule, options) File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 577, in post_process options, File "/home2/yjcho/phenix-1.3-final/elbow/elbow/utilities/optimisation_manager.py", line 331, in optimisation_manager pre_opt)) File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 857, in WritePDB original_order=original_order, File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 965, in WritePDB2String self.AdjustHydrogenNames() File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 940, in AdjustHydrogenNames if test_name[3]==" ": test_name[3]="0" TypeError: 'str' object does not support item assignment FYI. ADP is names as ADP as a residue name in the pdb file but has different chain names. By the way, I should mention that I used phenix.reduce first for adding H atoms but it was not able to add sugar H's in ADP molecule albeit other residues were fine. Thanks in advance for your help. Best, YoungJin

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Bulk solvent
by csantiag＠cnb.csic.es 03 Dec '08

03 Dec '08

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 ------------------------------------------------------------------------ César Santiago Dept of Macromolecules Structure Centro Nacional de Biotecnología, CSIC Campus Cantoblanco 28049 Madrid Spain csantiag(a)cnb.csic.es

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anomalous scatters refinement
by Daniele de Sanctis 02 Dec '08

02 Dec '08

Hi, I'm making some refinement tests with anomalous data and I wanted to try to refine the anomalous contribution. When would it be the best stage when to introduce it? Thanks D -- Daniele de Sanctis, PhD Macromolecular Crystallography Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

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phenix.autobuild- multiple models
by meindert lamers 29 Nov '08

29 Nov '08

Hi all, I am a bit puzzled by an error message I get when trying to run phenix.autobuild. (I am using the latest/final version of phenix: PHENIX VERSION: 1.3 of 11-08-2008) phenix.autobuild data=01.mtz model=3mei_coot.pdb multiple_models=True include_input_model=True \ multiple_models_number=1 n_cycle_rebuild_max=5 This gives me: **************************************** AutoBuild Input failed Sorry, multiple_models is only available with rebuild_in_place **************************************** However, when I run the same commands using an older version of phenix (PHENIX VERSION: 1.3 of 23-03-2008), all runs fine. Any ideas ? Meindert

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R/Rfree from phenix.autobuild
by Graeme Winter 28 Nov '08

28 Nov '08

Hi Folks, Quick question about R/Rfree from phenix - I ran the autobuild and it kindly built pretty much all of the visible residues, and it gave me the following output: SOLUTION CYCLE R RFREE BUILT PLACED 1 1 0.22 0.23 169 169 2 2 0.21 0.23 170 170 3 4 0.22 0.23 170 170 Now, I'm not one to complain about good results, but I did feel that the Rfree looked a little close to the R factor - usually I would expect a difference of maybe 4-5%. Is there a reason for this that I am missing? The model seemed to fit very nicely, closely corresponded to the PDB entry and the waters were pretty good. There is no NCS (one copy in the ASU) and the phases are from SeMet mad data from Autosol. Resolution is ~1.6A, if that is any help. Just noticed this and thought it was interesting. I am used to Arp/wArp for automated tracing, which typically gives a bigger difference... Many thanks, Graeme

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0 for wxc_scale and wxu_scale?
by Michaela Kramer, Biochemisches Inst. 26 Nov '08

26 Nov '08

I am refining a structure with a resolution of 2.1 Angstroem using Phenix. The spacegroup is P 31 2 1 (No. 152) with a twin fraction of 0.37 and twin law -h,-k,l. In the refinement procedure the NCS (4 chains) constraints are on, using individual sites, ADP and occupancy refinement. In the last refinement step, I use the option to optimize the values for wxu_scale and wxc_scale. These values are optimizes to 0 for wxc_scale and close to 0 for wxu_scale (0.2) When I tried this at earlier refinement stages wxu_scale was also here optimized in some refinement macrocycles to 0. Interestingly I obtain better R values (0.1948/0.2184), than without the optimization by using the default values (0.1391/0.2438 Rwork/Rfree). In addition to that the statistics are better: clashscore 14.41 (compared to 25.73 without wxc_scale & wxu_scale optimization), rotamer outliers 2.33% (compared o 4.66%) and Ramachandran favoured (Molprobity). How is it possible that wxu_scale and wxc_scale can be optimized to 0 by having better statistics? The total refinement target is defined as Etotal= wxc_scale x wxc x Exray + wc x Egeom As I understand it, the crystallographic refinement target (Exray) would now not be considered in the refinement procedure. Would this refinement procedure be valid? And how is wxc (output of target weights: x-ray data) defined? Thank you very much for your help Michaela Here is the output belonging to the optimization: Refinement Macrocycle 1 of 3 ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.649809 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 93.128 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.888942 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 85.407 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== Start r_free = 0.2118 scale= 0.0000 total_weight= 0.0000 r_free= 0.2181 0 scale= 1.0000 total_weight= 1.6498 r_free= 0.2336 0 scale= 1.5000 total_weight= 2.4747 r_free= 0.2379 1 scale= 2.0000 total_weight= 3.2996 r_free= 0.2412 2 scale= 0.6667 total_weight= 1.0999 r_free= 0.2297 0 scale= 0.5000 total_weight= 0.8249 r_free= 0.2245 1 scale= 0.4000 total_weight= 0.6599 r_free= 0.2226 2 Best r_free = 0.2181 ================================ ADP refinement =============================== ----------Individual ADP refinement---------- Start r_free = 0.2181 scale= 0.0000 total_weight= 0.0000 r_free= 0.2247 0 scale= 1.0000 total_weight= 0.8889 r_free= 0.2262 0 scale= 1.5000 total_weight= 1.3334 r_free= 0.2293 1 scale= 2.0000 total_weight= 1.7779 r_free= 0.2310 2 scale= 0.6667 total_weight= 0.5926 r_free= 0.2236 0 scale= 0.5000 total_weight= 0.4445 r_free= 0.2221 0 scale= 0.4000 total_weight= 0.3556 r_free= 0.2208 0 scale= 0.3333 total_weight= 0.2963 r_free= 0.2203 0 scale= 0.2857 total_weight= 0.2540 r_free= 0.2195 0 scale= 0.2500 total_weight= 0.2222 r_free= 0.2191 0 scale= 0.2222 total_weight= 0.1975 r_free= 0.2186 0 scale= 0.2000 total_weight= 0.1778 r_free= 0.2183 0 Best r_free = 0.2183 Refinement Macrocycle 2 of 3 ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.737535 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 89.612 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.228155 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 155.392 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== Start r_free = 0.2179 scale= 0.0000 total_weight= 0.0000 r_free= 0.2223 0 scale= 1.0000 total_weight= 1.7375 r_free= 0.2272 0 scale= 1.5000 total_weight= 2.6063 r_free= 0.2310 1 scale= 2.0000 total_weight= 3.4751 r_free= 0.2332 2 scale= 0.6667 total_weight= 1.1584 r_free= 0.2267 0 scale= 0.5000 total_weight= 0.8688 r_free= 0.2258 1 scale= 0.4000 total_weight= 0.6950 r_free= 0.2269 2 Best r_free = 0.2223 ================================ ADP refinement =============================== ----------Individual ADP refinement---------- Start r_free = 0.2223 scale= 0.0000 total_weight= 0.0000 r_free= 0.2228 0 scale= 1.0000 total_weight= 0.2282 r_free= 0.2235 0 scale= 1.5000 total_weight= 0.3422 r_free= 0.2256 1 scale= 2.0000 total_weight= 0.4563 r_free= 0.2275 2 scale= 0.6667 total_weight= 0.1521 r_free= 0.2219 0 scale= 0.5000 total_weight= 0.1141 r_free= 0.2213 0 scale= 0.4000 total_weight= 0.0913 r_free= 0.2207 0 scale= 0.3333 total_weight= 0.0761 r_free= 0.2204 0 scale= 0.2857 total_weight= 0.0652 r_free= 0.2201 0 scale= 0.2500 total_weight= 0.0570 r_free= 0.2197 0 scale= 0.2222 total_weight= 0.0507 r_free= 0.2195 0 scale= 0.2000 total_weight= 0.0456 r_free= 0.2194 0 Best r_free = 0.2194 Macrocycle 2 of 3 ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.157676 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 93.409 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.228399 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 140.390 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== Start r_free = 0.2163 scale= 0.0000 total_weight= 0.0000 r_free= 0.2189 0 scale= 1.0000 total_weight= 2.1577 r_free= 0.2299 0 scale= 1.5000 total_weight= 3.2365 r_free= 0.2340 1 scale= 2.0000 total_weight= 4.3154 r_free= 0.2341 2 scale= 0.6667 total_weight= 1.4385 r_free= 0.2282 0 scale= 0.5000 total_weight= 1.0788 r_free= 0.2255 1 scale= 0.4000 total_weight= 0.8631 r_free= 0.2249 2 Best r_free = 0.2189 ================================ ADP refinement =============================== ----------Individual ADP refinement---------- Start r_free = 0.2189 scale= 0.0000 total_weight= 0.0000 r_free= 0.2218 0 scale= 1.0000 total_weight= 0.2284 r_free= 0.2231 0 scale= 1.5000 total_weight= 0.3426 r_free= 0.2250 1 scale= 2.0000 total_weight= 0.4568 r_free= 0.2272 2 scale= 0.6667 total_weight= 0.1523 r_free= 0.2215 0 scale= 0.5000 total_weight= 0.1142 r_free= 0.2209 0 scale= 0.4000 total_weight= 0.0914 r_free= 0.2201 0 scale= 0.3333 total_weight= 0.0761 r_free= 0.2197 0 scale= 0.2857 total_weight= 0.0653 r_free= 0.2195 0 scale= 0.2500 total_weight= 0.0571 r_free= 0.2193 0 scale= 0.2222 total_weight= 0.0508 r_free= 0.2191 0 scale= 0.2000 total_weight= 0.0457 r_free= 0.2190 0 Best r_free = 0.2190 Michaela Kramer PhD student Institute of Biochemistry Winterthurerstrasse 190 8057 Zuerich Switzerland

7 6

trouble in phenix.refine
by Huiying Li 26 Nov '08

26 Nov '08

I was running phenix.refine in tls mode with the following command line: phenix.refine mydata.mtz mymodel.pdb strategy=tls tls_group_selection.param mylibrary.cif against a 2.1A data set, P21211 SG, a homodimer in AU, totally 10 tls groups. The following errors occured and program stopped. I do not know how to fix the problem. Traceback (most recent call last): File "/usr/local/phenix-1.3-final/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line 68, in run log=log) .... ... .... File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/monomer_library/pdb_interpretation.py", line 970, in get_lib_link atom_dicts[angle.atom_3_comp_id].get(angle.atom_id_3, None)] IndexError: list index out of range Your help is highly appreciated. Huiying -- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: hli(a)uci.edu

2 2

twin axis for p21
by HUA YUAN 25 Nov '08

25 Nov '08

Dear Colleagues, I'd like to share with you with a twinning puzzle that's been troubling me for a while. I have a ~2.2 A data merged in p212121 space group with unit cell: 41.8300 117.4490 134.4840 90.0000 90.0000 90.0000 Translational NCS was detected but structure solution was able to be obtained by phased molecular replacement as we have a Au derivative data set. Obtaining experimental phase or MR alone didn't work. However, with this model and data set, the refinement didn't work (with R-free ~40% or higher if with more cycles). Different twinning tests have been carried out and no sign of twinning. All possible p222 space groups have been tried but no luck or even worse. Considering that translational symmetry and perfect twinning may make things deceiving, the data was merged into p21 and a twin-refinement was performed in phenix.refine. After 3 cycles of rigid-body and group ADP, a R-free of ~30% was obtained and the output map looks OK. It looks like we got it. But then things get interesting when we tested other two axis as the p21 unique axis. With all the three choices plus corresponding twin-refinement, we could get a similar R-free (30%). Besides, the three maps all look OK except for one missing some side chains. Then the structure was solve in p1 and Xtriage was used with the hope that one axis would stand out. However, the RvsR for all three axis are almost the same. Did I miss anything here? Of course, we could pick up the one axis we like best and get the structure solved ^---^. However, this puzzle would eat me alive for a very long time. Best, Hua

2 1

solvent flipping
by Mark Collins 24 Nov '08

24 Nov '08

Hi Is there a solvent flipping (like solomon, ccp4) rather than flattening option in phenix? Mark

4 3

Windows version of Phenix
by Graeme Winter 21 Nov '08

21 Nov '08

Hi Folks, This is a potentially heretical question I know, but are there any plans to port Phenix to Windows in the future? Certainly having access to the command-line versions of the autosol and autobuild wizards would be excellent... Thanks, Graeme

2 1

Question about overall_best history
by Mo Wong 20 Nov '08

20 Nov '08

Hi all, I'm sure this is in one of the log files (and written somewhere in the documentation), but I can't find which solve_*.mtz and which subsequent resolve_*.mtz were used to make overall_best_denmod_map_coeffs.mtz. Could someone please tell me where I may find it. Thank you

2 3

Difference Fouriers using AutoSol
by Mo Wong 14 Nov '08

14 Nov '08

Hi, I'm a new Phenix user, so please forgive me if I ask an obvious question... I have pretty good SIRAS phases from one derivative, and calculating difference maps for 2 other derivatives show decent peaks above 5 sigma in both these maps. I've tried to follow the MIR example, but no sites are found in the two other derivatives (I thought Phenix calculates difference Fouriers for other derivatives as soon as it finds sites in one of the datasets - but it doesn't appear to in my case). Anyway, the following is my effeort at trying to use the SIRAS phases of the good derivative and the 5sigma peaks in the 2 other derivatives to phase a better map. Please could someone advise me if this script won't do what I'd like it to (i.e., calulate difference Fouriers for derviatives 2 and 3, refine the HA sites that I've included, and calculate phases): cell 100.000 100.000 100.000 90.000 90.000 90.000 # cell params resolution 5.5 # Resolution solvent_fraction 0.47 input_seq_file seq.dat ##### READ IN DERIV 1 SIRAS PHASES ###### input_phase_file solve_4.mtz input_phase_labels FP SIGFP PHIB FOM HLA HLB HLC HLD ############### DERIV 2 ################# input_file_list nat.sca hg.sca # Native and deriv 2 nat_der_list Native Hg # identify files by ha type inano_list noinano inano # say if ano diffs to be used f_prime -2.1 f_double_prime 9.5 n_ha_list 0 6 # number of heavy-atoms sites_file hg-sites.xyz run_list start # read in datafiles for dataset run_list read_another_dataset # about to start a new dataset here ############### DERIV 3 ################# input_file_list nat.sca xe.sca # Native and deriv 3 nat_der_list Native Xe # identify files by ha type inano_list noinano inano # say if ano diffs to be used f_prime -0.1 f_double_prime 3.5 n_ha_list 0 11 # number of heavy-atoms sites_file xe-sites.xyz ########################################## Many thanks!

1 0

General user proposal deadline November 15
by Peter Zwart 13 Nov '08

13 Nov '08

Dear All, The deadline for general user proposals for PX beamtime at the ALS is comming up soon! At the BCSB, we have 5 beamlines for which you can apply for beamtime. At the Berkeley Center for Structural Biology (BCSB) we have recently completed a number of upgrades: Sector 8: Recent improvements include: * A high-accuracy microdiffractometer on BL 8.2.1, allowing for centering and viewing of very small crystals * Robotic automounters which can increase the screening throughput at the beamlines, and allows for the implementation of remote data collection. * A new large format (315mm active surface area) CCD detector on BL 8.2.1, facilitating data collection on large unit cell crystals Sector 5: Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons per second at 0.97 Angstrom. This wavelength is slightly above the Se K edge making them ideal for performing Se SAD experiments. Beamline 5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons per second, and the energy range of 5.0.2 has been extended to 17 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. Remote data collection for general users on sector 5 is currently being tested for a limited number of users. Please contact beamline staff for details. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to apply for next round of beamtime (Jan-Feb) at the Advanced Light Source, please submit a General User proposal by November 15, 2008. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. (Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime.) ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

1 1

Autosol: cell keyword
by Page, Rebecca 13 Nov '08

13 Nov '08

Hi phenixers: Is there a way to use the Autosol Wizard with unmerged data from Scalepack? I can't get it to recognize the 'cell' keyword. Thanks in advance, Rebecca

2 1

restricted simulated annealing
by Raja Dey 12 Nov '08

12 Nov '08

Dear Friends, How can I restrict simulated annealing in phenix on part of my molecule, say 2 chains out of 3 or part of a particular chain? Thanking you in advance for your reply... Raja

2 1

Failed to carry out AutoBuild
by Joao Renato Carvalho Muniz 12 Nov '08

12 Nov '08

Dear Phenix community, I started an AutoBuild run using the Phenix GUI (ver 1.3 final) on linux. However, I noticed 2 weird things: 1st, Phenix seems that can not handle with alignment between the residues from pdb and sequence.seq, flagging the "Rebuild in place not recommended as identity * fraction_aligned is 0.0%" message but still trying to build the structure with the option "include_input_model=False" I guess(?)... and 2nd, after quite a while I obtained the following error message: ******************************************************************************** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /someplace/somedir/somedir2/AutoBuild_run_2_/TEMP0/RUN_FILE_1' /someplace/somedir/somedir2/AutoBuild_run_2_/TEMP0/RUN_FILE_1.log: File exists. ******************************************************************************** The alignment between MR.1.pdb and sequence.seq should be something like 80%+! Also tried to run using the followed command line: phenix.autobuild data=MR.1.mtz model=MR.1.pdb include_input_model=True n_cycle_rebuild_max=5 seq_file=sequence.seq Same problem as above. Could anyone please tell me what to do to prevent this error and get phenix get its job finished? Many thanks in advance, Joao.

2 1

refine occupancies for MET/MSE double conformations
by Anastassis Perrakis 11 Nov '08

11 Nov '08

Hi there - I was pleased to read in the manual: if no selections are provided (refine.occupancies.individual=None and refine.occupancies.group=None) then phenix.refine by default will refine individual occupancies for atoms that have partial occupancy values in input PDB file (except zeros) and it will perform group constrained occupancy refinement for all atoms in alternative conformations. Occupancies of all other atoms will be fixed. If selections are provided (refine.occupancies.individual=atom_selection or refine.occupancies.group=atom_selection) then the selected atoms will be added to the list of atoms defined above (atoms with partial occupancies or those in alternative conformations). See this document for examples of atom_selection syntax. However, I want to refine my MET residues in double conformations, one as MET (AMET) and the other one as MSE (BMSE) with each 0.5 occupancy to start with. When I try that I get: == ----------Initial model statistics (before refinement)---------- ... |-Occupancies statistics------------------------------------------------------| Sorry: There are atoms with negative occupancies. Check input PDB file. === The PDB file has 0.5 and 1.0 occupancies only. I am also using: == refinement.refine.strategy=tls+individual_sites+individual_adp +group_anomalous refinement.refine.adp.tls="chain A" refinement.refine.adp.tls="chain B" refinement.main.number_of_macro_cycles=4 refinement.simulated_annealing.start_temperature=5000 refinement.refine.adp.individual.anisotropic =" chain C" refinement .input .xray_data .labels=I_Mystery(+),SIGI_Mystery(+),I_Mystery(-),SIGI_Mystery(-),merged refinement.refine.anomalous_scatterers { group { selection = "name ZN " f_prime = -0.3 f_double_prime = 2.5 refine = *f_prime *f_double_prime } group { selection = "name SE " f_prime = -5.2 f_double_prime = 3.8 refine = *f_prime *f_double_prime } } == Any hints on how to proceed ? Should I define groups for the occupancy refinement explicitely and not rely to automatic assignment? And if so how? How do people treat this partial Se-Met issue ? We solved the structure with SeSAD ... if I out MSE I get pretty large negative density peaks on the Se ... if I put MET I get positive peaks ;-) And there are good reasons to believe in partial Se- substitution in this case. Thanks in advance, Tassos

8 15

cis peptide
by Jianghai Zhu 09 Nov '08

09 Nov '08

Hi, Does phenix.refine restrain cis peptide? How do I know if the refined pdb file contain any cis peptide? Thanks. -- Jianghai

3 3

User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 05 Nov '08

05 Nov '08

Dear Users, Through the Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source, scientists can send protein crystals to Berkeley Center for Structural biology (BCSB) staff researchers for data collection and analysis. The CC Pilot Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ============= How To Apply: To submit a proposal, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html Click on "protein crystallography" to begin proposal. For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for January/February 2009 allocation period, proposals must be submitted by November 15, 2008. The deadline for CC proposals for the time period March/April 2009 will be January 15, 2009. Regards, Banumathi Sankaran

1 0

weight optimization
by Raja Dey 03 Nov '08

03 Nov '08

Hi, I was trying to optimize weights as follows, but it came out with the error given below. Can anyone tell me what's wrong? I used phenix.refine ../p65_nat.mtz ../p65_136.1.pdb optimize_wxc=true optimize_wxu=true output.prefix=136.1 ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder' Thanks... Raja

6 6

DNA sugar pucker
by Laura Murray 26 Oct '08

26 Oct '08

Hi. I'm one of the Richardsons' people. I have more experience with RNA, but have looked at DNA some as well. 1. On C2'-endo and C3'-exo being equivalent: no, not quite equivalent, but related. If you do have C1', C4', and O4' in the plane, then "popping" C2' out on one side or C3' out on the other is relatively similar (sort of) and there's a recognized "twist" conformation where you've got them both out of plane a bit. However, you can really get C3' mostly in-plane with the other three and have a conformation that's distinctly a C2' endo pucker rather than looking like it could be either one. If you're building ideal B-form DNA, it would be better to use a real C2'-endo pucker than the twist, and certainly better than using the C3'-exo. 2. I'm afraid I don't know the appropriate format for use with PHENIX, but there are pucker-specific parameters available on the Nucleic Acid Database site: http://ndbserver.rutgers.edu -- specifically, here: http://ndbserver.rutgers.edu/standards/parameter.html -- these are set up for XPLOR, but the values should help. At any rate, these files distinguish the dihedrals for C2'-endo and C3'-endo sugar puckers. (The set for higher resolution also provides slightly different bond lengths and angles for them, since the ring strains are a bit different.) And I don't think they make a habit of turning up C3'-exo. Laura Murray

1 0

sugar puckering in an ideal B-DNA
by chern 26 Oct '08

26 Oct '08

Hi all, does anybody know why coot and sybil (and may be others that I don't know about) generate an ideal dna with C3*-exo puckers instead of C2*-endo, as text books say. maia

2 1

phenix.refine output map format
by Paul Emsley 24 Oct '08

24 Oct '08

Dear Phenixers, Is is possible for phenix.refine to output a ccp4 map? If so, how? Thanks, Paul.

5 8

elbow
by chern 24 Oct '08

24 Oct '08

Dear all, could I use eLBOW to create a .cif file for a B-DNA to restrain sugar puckers? Maia

4 6

sugar puckering in DNA
by Maia Cherney 24 Oct '08

24 Oct '08

Hi Yu Seon. I would appreciate it very much if you send me your added restraints to the cif file. Maia YS. Chung wrote: > Hi Maia, > I had the same problem when I was refining with phenix. I ended up > looking at the torsions that were used in 3DNA (the program I used to > analyze the puckerings) and manually added the restraints to the .cif > files used in phenix. I can send you an example if you'd like. The > puckerings improved a lot when I used the modified .cif files. > Yu Seon > > On Fri, 24 Oct 2008 10:43:44 -0600 > "chern" <chern(a)ualberta.ca> wrote: > >> Sorry, I gave a wrong subject name in my previous e-mails. Should've >> been sugar puckering in DNA. >> I am wondering why the default .cif file for DNA does not include all >> >> information about sugar puckers. >> I do not have some fancy nucleotides. They are regular. >> >> Maia >> >> ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" >> <rwgk(a)cci.lbl.gov> >> To: <phenixbb(a)phenix-online.org> >> Sent: Friday, October 24, 2008 10:03 AM >> Subject: Re: [phenixbb] elbow >> >> >> >>>> The answer is yes but there may be better options. Ralf is the >>>> >> best >> >>>> person to answer this question but one option is to start with the >>>> >> .cif >> >>>> file in the monomer library. >>>> >>> This is more a chemistry question than a formatting question. >>> Since I'm not deeply familiar with the DNA chemistry, I was >>> >> pointing >> >>> Maia to phenixbb in hopes that someone may already have figured out >>> the list of torsion angle restraints to fix sugar puckers. >>> >>> What Maia really wants is: >>> >>> >>>> could you please send me a specific example of how to modify a cif >>>> >> file >> >>>> to specify the sugar puckers in DNA (I want them C2'-endo). >>>> >>> Has anyone on this list done this already? >>> >>> Ralf >>> _______________________________________________ >>> 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 >> > >

1 0

Re: [phenixbb] phenix.autobuild
by Matthew Chu 24 Oct '08

24 Oct '08

Thank you for the detailed information Tom, my autobuild job is actually running properly! Just some more minors questions: 1. AutoBuild Wizard will use phenix.elbow to generate geometries for any ligands that are not recognized, but how can I find out which ligands that can actually be recognized by phenix? Or to be save, we better run elbow to generate the libraries for every single ligands? 2. eLBOW can automatically add hydrogens to the input molecules if there are less than a quarter of the possible hydrogens, however this command doesn't work: phenix.elbow input_file.pdb --add-hydrogens=True, and I can't find this option under the elbow manual? And actually I would like to remove those hydrogens so it should be "add-hydrogens=false"? I am now using phenix-1.3-rc2. Thanks again! Matt -- ---------------------------------------------------------------------------- Matthew LH Chu PhD Student School of Pharmacy and Pharmaceutical Sciences University of Manchester ----------------------------------------------------------------------------

3 3

NAG-ASN link geometry
by nihmayerm 23 Oct '08

23 Oct '08

We are refining a 2.7 A structure with multiple ASN-NAG links using phenix-1.3-final. The torsion angle between the Asn amide and the sugar is quite variable, while from the chemistry of this link we would expect a value close to 180°, as reported in the PDB survey by Imberty & Perez (Protein Engineering 8:669-709). A quick look at some entries in the PDB revealed close to textbook geometry for the NAG-ASN link in structures around 1Å resolution (e.g. 1UWC) and gets much worse in some lower resolution structures, including those refined with PHENIX. The NAG-ASN link used by PHENIX does not contain a torsion angle definition, and I would like to ask (i) if its appropriate to use one in refinement, and if so (2) could people share their cif file for this link. Thanks - MLM

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optimize weights error
by Sean Johnson 23 Oct '08

23 Oct '08

I just tried optimizing weights in phenix.refine using optimize_wxc=true and optimize_wxu=true in the command line. I got the following error: ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc5/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc5/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc5/phenix/phenix/refinement/driver.py", line 1150, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc5/phenix/phenix/refinement/strategies.py", line 446, in refinement_machine log = log) File "/usr/local/phenix-1.3b-rc5/phenix/phenix/refinement/weight_xray_chem.py", line 252, in __init__ self.wxc_optimization() File "/usr/local/phenix-1.3b-rc5/phenix/phenix/refinement/weight_xray_chem.py", line 507, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder' Any suggestions? Thanks, Sean -- Sean Johnson, PhD R. Gaurth Hansen Assistant Professor Utah State University Department of Chemistry and Biochemistry 0300 Old Main Hill Logan, UT 84322-0300 (435) 797-2089 (435) 797-3390 (fax) sean.johnson(a)usu.edu

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phenix.autobuild
by Matthew Chu 22 Oct '08

22 Oct '08

Dear all, I tried to rebuild my structure from a refined model (by refmac) by phenix.autobuild. I am not sure if it runs properly since this is my first time to run this module....it took like almost a day to just finish the run_1 (there should be five runs by default?), which means it will take me another 4 days to finish the whole thing. My protein has around 350 residues and in the refined model, I have omitted some loops (about 80 residues) because I cannot see the electron density of those regions. I have put the seq.dat file with the full sequence (~350 residues) and the commands "place_water=Yes" and "s_annealing=True". The resolution is 2.4 A. Should it be taken so long to run? Thanks in advance! Kind regards, Matt -- ---------------------------------------------------------------------------- Matthew LH Chu PhD Student School of Pharmacy and Pharmaceutical Sciences University of Manchester ----------------------------------------------------------------------------

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phenix.pdbtools question
by Simon Kolstoe 21 Oct '08

21 Oct '08

Dear phenix list, I am wanting to model a poly-proline structure. I created the file in PyMOL, saved it as a pdb, and then tried to regularize it with: phenix.pdbtools polypro.pdb --geometry_regularization However the program reported (snipped to the last few lines): ATOM 63 CD PRO 6 -3.290 3.487 -2.968 1.00 0.00 C ATOM 69 2HD PRO 6 -2.824 2.626 -3.453 1.00 0.00 H Distance model: 1.09209 (ideal: 0.97) ATOM 63 CD PRO 6 -3.290 3.487 -2.968 1.00 0.00 C ATOM 70 3HD PRO 6 -4.165 3.171 -2.396 1.00 0.00 H Distance model: 1.44721 (ideal: 1.473) ATOM 57 N PRO 6 -2.321 4.145 -2.118 1.00 0.00 N ATOM 63 CD PRO 6 -3.290 3.487 -2.968 1.00 0.00 C Distance model: 1.53855 (ideal: 1.525) ATOM 58 CA PRO 6 -1.810 5.407 -2.632 1.00 0.00 C ATOM 59 C PRO 6 -2.332 6.603 -1.817 1.00 0.00 C Distance model: 1.23088 (ideal: 1.231) ATOM 59 C PRO 6 -2.332 6.603 -1.817 1.00 0.00 C ATOM 60 O PRO 6 -3.080 6.424 -0.856 1.00 0.00 O Sorry: Number of bonds with excessive lengths: 74 I thought the whole purpose of geometry regularization was to get rid of excessive lengths, not just tell me they are there!! How do I get the program to really regularize my geometry? Thanks, Simon

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phenix.reduce (v1.3) changes
by Mark Collins 21 Oct '08

21 Oct '08

Hi Did the --ALLALT command change. I thought the --help gave the flag description as "builds hydrogens for all conformations" but no it says "process adjustments for all conformations" And by default (-ONLYA) so I only have conf A with hydrogens using the --ALLALT flag. Long and short of it I think something is up? Thanks Mark

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postdoc position in LBNL
by Peter Zwart 20 Oct '08

20 Oct '08

Dear All, We would like to bring the following postdoctoral research position to your attention. Within Lawrence Berkeley Laboratory, we have an opening for a postdoc to work on the development of new software for the analysis of small angle X-ray scattering (SAXS) data. The availability of user friendly, robust software analysis tools for SAXS data is of growing importance as the biological community is increasingly using SAXS as a standard method to analyze complex biological systems. We are developing a new set of tools, including a software library, for SAXS data analysis. The successful candidate will have the opportunity to work with experienced software developers in the field of biophysics and interact with users and beamline staff on SAXS beamline 7.3.3 at the Advanced Light Source (ALS) in Berkeley California. Interested candidates can contact me (Peter Zwart, PHZwart(a)lbl.gov) for more details, or visit the LBL job site at: http://jobs.lbl.gov/ Sincerely, Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Twin refinement with anomalous pairs
by Francis E Reyes 20 Oct '08

20 Oct '08

All How does phenix.refine handle the twin refinement target when refining against F+/F-? I'm specifically asking for the proper assignment of F +/F- for twin related reflections (e.g. 10.1107/S0907444902021704). My data is currently in P41 with friedel pairs as output by scala. Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Re: [phenixbb] sa_omit-map
by mathieu Coincon 18 Oct '08

18 Oct '08

Hi, omit-map works fine for me but I have two items on my wish list. 1) Can we compute a difference-map (mFo-DFc map instead of 2mFo-DFc map) ? 2) Is it possible to play with the size of the area omitted around the selection ? Thanks again. A true phenix-fan -------------- Mathieu Coincon PhD Student Universite de Montreal Biochemistry 514-343-6111 #5352

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phenix.refine: including modifications
by Patrick Loll 17 Oct '08

17 Oct '08

Hi all, I'm starting to use phenix.refine and have some questions about defining modifications during refinement: I want to refine a structure that includes several alpha-D-mannose residues. I see that mon_lib_list.cif contains, under the "LIST OF RECOGNIZED MODIFIED MONOMERS," the following line: MAN-a-D MAN-b-D SUG-a-D MAN alpha_D_mannose D-pyranose Question: Where/how do I invoke this modification? I.e., how do I tell the refinement program that a particular sugar is an alpha, and not a beta, mannose? Clearly I can't label the residue MAN-a-D in the PDB file, as this would step on the chain identifier. I'm guessing that I label each sugar MAN in the PDB file, and then insert some instructions about applying the modification in the CIF file that I supply to the refinement program. However, I'm not able to find an example of the appropriate syntax. Thanks, Pat Loll ------------------------------------------------------------------------ --------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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Hydrogen occupancy issue?
by Mischa Machius 17 Oct '08

17 Oct '08

Hi - I have a problem regarding occupancies of hydrogens in residues with alternate conformations. Specifically, when a residue exists in alternate conformations, the H hydrogen of the following residue (the one attached to the N) also exists in the same number of alternate locations. The occupancies of these hydrogens do not add up to 1.00 like the occupancies of the hydrogens for the preceding residue do. In fact, these occupancies are all 1.00. Is that a bug, a feature, or did I commit a user error somehow? Example: ... ATOM 956 H AHIS A 293 6.967 -36.722 8.227 1.00 15.31 H ATOM 957 H BHIS A 293 6.913 -36.667 8.216 1.00 15.31 H ATOM 958 H CHIS A 293 6.888 -36.648 8.202 1.00 15.31 H ... The preceding Ser A 292 exists in three alternate conformations with occupancies A=0.53, B=0.18, C=0.29; sum = 1.00 The corresponding hydrogens have occupancies A=0.52, B=0.19, C=0.29; sum = 1.00 (I can accept that they have somewhat different occupancies than the attached heavy atoms, based on a previous thread about this issue, although the discrepancies are now much smaller in the 1.3- final version compared to 1.3-rc2) The H hydrogens of the following residue (His A 293) have occupancies A=1.00, B=1.00, C=1.00; sum = 3.00, and the RCSB starts yelling. Should I just manually edit the values and set them to the occupancies of the hydrogens in the preceding residue? Any help appreciated. Thanks so much. Best - MM -------------------------------------------------------------------------------- Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353

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Weighted phase combination in phenix.refine?
by Francis E Reyes 17 Oct '08

17 Oct '08

Hi all I have experimental phases and a preliminary model. Will phenix.refine do phase combination while weighting the experimental phase and model phases (which also has NCS) ? By default? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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high temperature factor refinement
by allbette＠gmail.com 17 Oct '08

17 Oct '08

Hi All, I just refined a structure at 2.95A and getting a good R-work and R-free(0.236 and 0.274). When I checked the PDB, I found many residues have high temperature factor over 100. How can I use Phenix or CNS fix those high temperature factor for further refinment? Thank you Jason

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