- phenixbb - phenix-online.org

riding hydrogens
by Jianghai Zhu 06 Aug '08

06 Aug '08

Hi, I used phenix.reduce to add riding hydrogens. After phenix.refine, the structure got a good score from MolProbity. However, if I stripped the riding hydrogens from the structure and let MolProbity to add hydrogens before the analysis, I got a much worse score, especially the clash score. Does phenix.refine refine the hydrogen positions? -- Jianghai

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DNA restraints
by jens j birktoft 06 Aug '08

06 Aug '08

Hi, Is there a way to restrain selected hydrogen bonds between base pairs during the refinement of DNA structures ? CNS has something like DNA_RNA.def if I remember correctly and I am looking for something of that nature. Cheers Jens -- Jens J. Birktoft - e-mail: jens.knold(a)gmail.com slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 use 212-749-5057 for ALL phone calls

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Deborah Palestrant is out of the office.
by deborah.palestrant＠novartis.com 05 Aug '08

05 Aug '08

I will be out of the office starting 08/05/2008 and will not return until 08/11/2008.

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torsion angle dynamics simulated annealing?
by Bryan W. Lepore 04 Aug '08

04 Aug '08

i was wondering if someone could comment on any possibility of implementing torsion angle dynamics in phenix's simulated annealing procedure, in a future release of phenix? i.e. is that "in the works"? thanks! -bryan 1

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phenix.refine: Override 'Number of bonds with excessive lengths'
by Martin.Laurberg 04 Aug '08

04 Aug '08

Dear All, Is there a way to override the phenix.refine Setup Restraints Manager, preventing phenix.refine from terminating if the model features a lot of excessive bond lenghts? Thanks, /Martin ========================== Set up restraints manager ========================== .... Bonds with excessive lengths: Distance model: 50.2364 (ideal: 1.525) ATOM 1336 C3' DC B 20 12.611 28.560 12.463 1.00 42.81 C ATOM 1338 C2' DC B 20 -11.801 15.989 54.531 1.00 42.03 C .... Sorry: Number of bonds with excessive lengths: 71 -- Martin Laurberg, PhD Noller Laboratory 225 Sinsheimer Laboratories University of California at Santa Cruz CA-95064 Santa Cruz USA Tel +1 (831) 459 35 84 Fax +1 (831) 459 37 37

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Wishful thinking with AutoBuild?
by Francis E Reyes 04 Aug '08

04 Aug '08

Hello all Given a mediocre to bad experimental density map, what hopes does AutoBuild have of building a model? i.e. Should I be able to tell clear helicies and side chain density in the experimental density map before even attempting an autobuild? 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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GUI inactivity
by David Hoover 04 Aug '08

04 Aug '08

We have RedHat Enterprise Linux 5, and the Phenix installation went just fine. When I fired up the GUI, it looked ok, but the inset was blank. Many of the buttons seemed inactive as well. Is there any support for installation beyond that on the web page? David Hoover, Helix Systems Staff, CIT/NIH

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Ordered solvent - wish list
by Jendrek 04 Aug '08

04 Aug '08

Hi All, On the matter of ordered solvent I was just wondering if fixing specific waters (like ones close to metals) was implemented in the latest release. Also, it would be a nice touch if the water list was ordered according to some criteria. In my lab we prefer to have them in decreasing B factors - but that is just wishing... Regards, Andrzej -- Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[(a)]helsinki[.]fi) Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65 - Viikinkaari 1 Floor/Room: 4/4316 Mail: FIN-00014 University of HELSINKI, FINLAND Delivery: FIN-00710 University of HELSINKI, FINLAND TEL.: 358 9 191 58921 FAX : 358 9 191 59940

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ordered solvent - parameters?
by Mark Collins 31 Jul '08

31 Jul '08

Hi All I was just going through the .help section and website documentation for ordered_solvent. And wonder if somebody could enlighten me as too the meanings of; ordered_solvent { primary_map_type = mFobs-DFmodel secondary_map_type = 2mFobs-DFmodel h_bond_min_mac = 1.8 h_bond_min_sol = 1.8 h_bond_max = 3.2 } peak_search { map_next_to_model { use_hydrogens = False } max_number_of_peaks = None peak_search { peak_search_level = 1 max_peaks = 0 interpolate = True min_distance_sym_equiv = None general_positions_only = False min_cross_distance = 1.8 } What is the difference between the primary and secondary map? Is there away to pick sites in one and remove in another? Eg. pick sites at 3 sigma in FoFc and remove if 1.2 sigma in 2FoFc. I thought h-bonding was generously about 2.4-3.6A so why the 1.8 and 3.2 defaults? Also if use_hydrogens = True, does the refinement use h_bond parameters instead of model_peak_dist and peak_peak_dist parameters, or both? Also what do all of the peak_search parameters do? And finally does anyone have any recommendations for progessively changing the ordered_solvent parameters? In CNS we used to gradually lower the 2FoFc peak picking (and deleting) and increase the bfactor_max for deleting? Thanks Mark

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Maintaining the sugar puckerings
by YS. Chung 31 Jul '08

31 Jul '08

Hi all, I have a protein-DNA structure at 3 angstroms that I have been refining with refmac5. I have recently started to look into using phenix.refine instead. However, I am still having some problems with the sugar puckering of my DNA which is an ideal B-DNA and should be kept C2'-endo, but keeps changing to C1'-exo or C3'-endo after refinement with phenix. I have looked at the .cif files for the DNA and may update the restraints. Is this the easiest way to go about restraining the sugar puckering? Thank you, Yu Seon Chung

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calculating a phased anomalous difference map for twinned data in phenix.refine
by Michael Hothorn 31 Jul '08

31 Jul '08

Hi, to confirm the nature of a metal ion in my active site, I want to calculate a phased anomalous difference map in phenix.refine. However my crystals in SG P3(2) are twinned with twin law h,-h-k,-l and a fraction of about 40%. Is there a way to calculate an informative map in phenix.refine in this case? best Michael

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SA-omit maps for carbohydrates
by Enrico Girardi 30 Jul '08

30 Jul '08

Dear All, I would like to create a SA-omit map for two carbohydrate chains present in my structure. My attempts using the command phenix.autobuild data=data.mtz model=final.pdb omit_box_pdb=cho2.pdb composite_omit_type=sa_omit lead to a message in the log file saying: Failed to carry out AutoBuild_set_up_build: Sorry, unable to define an omit region with cho2.pdb res_start = None res end = None chain = '' ? Possibly no atoms? The procedure works fine with protein residues so I am assuming that phenix.autobuild is ignoring the sugars in the original pdb file (as it says in the log file..). Is this correct? How can I fix the problem? I am running Phenix 1.3b. Many thanks in advance for your help. Regards Enrico -- Enrico Girardi Randall Division of Cell and Molecular Biophysics King's College London New Hunt's House Guy's Campus London SE1 1UL Tel +44 (0)20 7848 6419 Fax +44 (0)20 7848 6435

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New PHENIX prerelease 1.3-rc4
by Paul Adams 28 Jul '08

28 Jul '08

Dear PHENIX Users, there is a new prerelease of PHENIX available (1.3, release candidate 4). It can be downloaded from the PHENIX web page as usual: http://www.phenix-online.org/ Cheers, Paul -- 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: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Administrator: Delia Clark [ DNClark(a)lbl.gov ][ 1-510-486-6331 ] --

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phenix.automr
by Ivan Campeotto 28 Jul '08

28 Jul '08

Dear All, I am trying to use Phenix AutoMR followed by Autobuild. The problem is that in the output file "overall_best_refine_map_coeffs.mtz" from Autobuild the Fc values have been set to zero. The Fc values are not zero in the output file MR.1.mtz coming from AutoMR if it may be of help. Any suggestion to fix this problem will be appreciated. Thank you in advance Ivan

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phenix.automr problem
by allbette＠gmail.com 25 Jul '08

25 Jul '08

Dear all I tried to solve a structure by using phenix.automr. I am not sure how many molecules in the asymmetric unit(2-8molecules). How I can tell phenix.automr (phaser) that search at least 2 molecules in asymmetric unit use command line. Any suggestions are welcome.Thank you in advance. carl soja

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Re: [phenixbb] autobuild failed
by Thomas C. Terwilliger 23 Jul '08

23 Jul '08

Dear Kaituo, I'm sorry for the problem! I'm not certain what went wrong in this case. It could be that the size of the structure is too big, or it could be a problem with autobuild, or it could be a problem with slow read/write to your file system. The error message "Unable to read ok_file...trying bigger version" will occur if resolve does not finish writing out the file "resolve.ok" immediately after finishing. If you are running on a system that is NFS-mounted, you might try instead running on the local disk. This might fix it. Otherwise, can you help me figure this out by eliminating other possibilities: 1. Can you tell me the version of phenix you are using and what machine this is on: echo $PHENIX_VERSION uname -a 2. Can you send me the entire log file AutoBuild_run_1_1.log 3. Can you send me the file AutoBuild_run_1_/TEMP0/temporary.com 4. If you are willing to send your data, that would be helpful: just tar up your data files and command file and then attach it to an email (but rename the file ".txt" so that it will get sent properly through my email system). Then I can try to reproduce the problem here. All the best, Tom T > My autobuild failed and the log file said: > Columns used: labin FP=F SIGFP=SIGF FreeR_flag=FreeR_flag > Unable to read ok_file...trying bigger version > Failed to run resolve > ---------------------------------- > TRIED resolve ...but not OK > > ********************************************************************************Failed > to carry out AutoBuild_set_up_build: > failure > > how t solve this? > thanks > > kaituo > > peking University, Beijing > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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autobuild failed
by wang kaituo 23 Jul '08

23 Jul '08

My autobuild failed and the log file said: Columns used: labin FP=F SIGFP=SIGF FreeR_flag=FreeR_flag Unable to read ok_file...trying bigger version Failed to run resolve ---------------------------------- TRIED resolve ...but not OK ********************************************************************************Failed to carry out AutoBuild_set_up_build: failure how t solve this? thanks kaituo peking University, Beijing

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Re: [phenixbb] reflection files, anomalous data, and test set
by Ralf W. Grosse-Kunstleve 23 Jul '08

23 Jul '08

Hi Mark, > input { > xray_data { > file_name = ../testmtz.mtz > labels = "I(+),SIGI(+),I(-),SIGI(-)" > r_free_flags { > file_name = ../SePeak.hkl > label = TEST > test_flag_value = 1 }} Could you try this instead? xray_data { file_name = SePeak.sca labels = None r_free_flags { file_name = ../SePeak.hkl label = TEST test_flag_value = 1 }} Let me know if this gives the same error as before (could be). Ralf

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Final reminder: 2008 Crystallographic Computing School
by Ralf W. Grosse-Kunstleve 23 Jul '08

23 Jul '08

The registration deadline for the 2008 Crystallographic Computing School is in two days: *** July 25 *** The schedule of the program including abstracts from all speakers is available here: http://www.iucr.org/iucr-top/comm/ccom/kyoto2008/program.html This program puts a strong weight on fostering one-on-one interactions. There will be only 16 lectures of 45 minutes each (12 hours total) but more than 20 hours of tutorials and demonstrations. Don't miss this unique opportunity for close interaction with the developer community! On behalf of the organizing committee: A. L. Spek (Utrecht University , Netherlands) R. Grosse-Kunstleve (LBNL, USA) M. Yao (Hokkaido University, Japan) A. Nakagawa (Osaka Institute of Protein, Japan) H. Powell (MRC, UK) L. Cranswick (NRC , Canada)

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Creating files with positive and negative map peaks
by Jennifer Ekstrom 23 Jul '08

23 Jul '08

I would like to obtain a file with a listing of positive and negative difference map peaks, similar in formatting and content to the files that would come out of cns: positive peaks in: <output_root>_positive.peaks negative peaks in: <output_root>_negative.peaks We need this for use in DDQ at the jcsg validation server (http://www.jcsg.org/prod/scripts/validation/sv2.cgi). Is there an easy way to create these peak files in phenix.refine? We'd prefer to not re-refine in CNS as we have *many* alternate conformations... Thanks, Jennifer

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NCS constraints in phenix.
by colletier 19 Jul '08

19 Jul '08

Dear All Does a beta version of phenix.refine that would allow the use of NCS constraints exists somewhere ? Best Jacques Ph Colletier

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SIR with sites from SAD?
by Francis E Reyes 17 Jul '08

17 Jul '08

I have a SAD dataset where autosol was able to find sites, but the resulting density modified map was uninterpretable. The unit cell for this SAD set was Unit cell: (53.2373, 53.2373, 186.446, 90, 90, 90) . I now have a heavy atom derivative. What's the format of autosol.inp (to be passed to phenix.runWizard AutoSol) that allows me to use the heavy atom sites from the SAD set as a basis for helping find heavy atom sites in the heavy atom derivative? Is it the same as SIR, except use ha_sites_file for the SAD solution? Native unit cell: [53.155600000000007, 53.1556000 00000007, 187.37970000000001, 90.0, 90.0, 90.0 Derivative unit cell: [53.1 82299999999998, 53.182299999999998, 187.59569999999999, 90.0, 90.0, 90.0]. 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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Deborah Palestrant is out of the office.
by deborah.palestrant＠novartis.com 16 Jul '08

16 Jul '08

I will be out of the office starting 07/16/2008 and will not return until 07/21/2008.

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Anomalous difference map calcluation
by Jendrek 16 Jul '08

16 Jul '08

Dear All, I'm looking at my anomalous difference map from phenix.refine and it seems more or less random distributions of electron density peaks. I know that the signal is there since I solved it with SAD. I'm using I(+/-) for refinement and everything seems to work fine except the map generation. The only thing that worries me is that during the creation of _data file for refinement DANO column was not preserved. Is it necessary for phenix.refine in order to generate the anomalous difference map? How can I make sure that the DANO column is preserved (if necessary)? And by the way why is anomalous map file not generated just coefficients in the mtz? Regards, Andrzej -- Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[(a)]helsinki[.]fi) Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65, Viikinkaari 1 FIN-00014 University of HELSINKI, FINLAND TEL.: 358 9 191 58955 FAX : 358 9 191 59940

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Postodoctoral Position - Berkeley California
by Paul Adams 14 Jul '08

14 Jul '08

The Berkeley Center for Structural Biology (BCSB) has an opportunity for a Postdoc to develop hardware and software for the automated control of data collection instrumentation and methods for automated data collection and analysis. You will also provide technical and scientific help to users at the BCSB beamlines (http://bcsb.lbl.gov) at the Advanced Light Source in Berkeley California and participate on projects involving the structure determination of biological molecules and biomolecular complexes as required by users and other BCSB staff members. Responsibilities Under the direction of the Principal Investigator, you will: - Assist in the development of hardware and software for the automated control of data collection instrumentation and methods for automated data collection and analysis. - Participate in engineering projects to advance the capabilities of the beamlines, including robotics systems for sample handling. - Assist in the development of instrumentation and methodology for biological crystallography. - Participate in the design, implementation, and evaluation of collaborative experiments involving biological crystallography. - Participate in helping users regarding data collection, processing, archiving, and analysis. - Collaborate with colleagues both internal and external to the Berkeley Lab. Prepare documentation for beamline staff and users. - Prepare scientific data for publication in refereed journals and present findings at seminars and conferences. - Provide work oversight and direction to technical staff as needed (which will require occasional work off-hours and weekends). - Assist with developing research proposals that lead to continued funding in the area of biological crystallography for the BCSB/ALS. Key Qualifications - A recent Ph.D. in physics, biology, bioengineering, biophysics, or related field. - Experience working in the area of synchrotron science using complex instrumentation and computer controls. - Experience with robotics hardware and control systems. - Experience with the collection of experimental data for biological crystallography. - Demonstrated ability to conduct independent research and organize results for publication and presentation documented by publication record in either: physics, biology, bioengineering, biophysics, biochemistry or instrumentation fields. - Excellent written communication skills along with strong organizational, analytical, and interpersonal skills. - Experience in the use of computer programs required for biological crystallography. - The ability to work in a team environment and effectively interact with a broad range of colleagues. - Experience in UNIX computing is highly preferred. This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. How To Apply To apply please visit: http://jobs.lbl.gov/LBNLCareers/details.asp?jid=21987&p=1 Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce. -- 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: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Administrator: Delia Clark [ DNClark(a)lbl.gov ][ 1-510-486-6331 ] --

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