- phenixbb - phenix-online.org

Obtaining just the Wilson B with Xtriage
by Morten Grøftehauge 26 Mar '14

26 Mar '14

Hi guys, Is there a way to just have phenix.xtriage compute and output the Wilson B factor and not do everything else? I want to run it on a lot of files and that would simplify things. Cheers Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

3 3

2014 workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 25 Mar '14

25 Mar '14

Second announcement Fifth Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 16 - June 20, 2014 Application deadline: April 18, 2014 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization may not be able to offer travel or accommodation support. The number of participants will be limited to 15. There is no registration fees for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 18, 2014. Detailed information can be found on the course web page: http://neutrons.ornl.gov/conf/gcnb2014/ Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

1 0

xtriage reindexing suggestions
by Todd Jason Green 24 Mar '14

24 Mar '14

Hello all- I am trying to merge a few partial Se datasets. I am certain that I will have to reindex one or more to make sure that + and - reflections are not jumbled up. Can someone confirm that xtriage take this into account in suggesting to reindex one dataset in relation to a reference dataset? ie. does it use something like maximizing the anomalous signal in suggesting whether or not reindexing is necessary? I think the below suggests as much but I wanted confirmation: Automatic re-indexing For each data set supplied (other than the first data set given), all possible re-indexing matrices are derived as described by Grosse-Kunstleve et al. (2005). Each data set isautomatically re-indexed using the matrix that maximizes the correlation of amplitudes Have a good weekend. -Todd My Example: Reference analyses The following reindexing operators have been found: ------------------------------------------------- | Operator | Correlation | matches (%) | choice | ------------------------------------------------- | -k,h,l | 0.874 | 70.1 | <--- | | h,k,l | 0.032 | 76.7 | | ------------------------------------------------- If the data is reindexed with operator (-k,h,l), the correlation of the intensities to the reference data is maximized. sx205b_anom.sca This can be done for instance with: phenix.reflection_file_converter sx205b_anom.sca --change_of_basis="-k,h,l" <output_options>

4 4

Multiprocessor refine
by Kenneth A. Satyshur 23 Mar '14

23 Mar '14

The FAQ on the web says that phenix.refine uses multiprocessors, yet only phenix.autobuild seems to use MP. Do I need a special version of Phenix? I am using GUI 1.8.4-1496 >How can I use multiple processors to run a job? >Only AutoBuild(http://www.phenix-online.org/documentation/autobuild_gui.htm), LigandFit(http://www.phenix-online.org/documentation/ligandfit_gui.htm), phaser.MRage(http://www.phenix-online.org/documentation/MRage.htm), phenix.refine(http://www.phenix-online.org/documentation/refine_gui.htm), the structure comparison GUI(http://www.phenix-online.org/documentation/structure_comparison.htm), and phenix.find_tls_groups support runtime >configuration of parallel processing. In most cases this is done by adding the "nproc" keyword, for instance: etc RHEL6 x86_64 thanks kas -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

2 1

Fwd: Reminder: CCP4 crystallographic summer school in USA, at APS, June 24-July 2
by Nathaniel Echols 17 Mar '14

17 Mar '14

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Cc: Date: Mon, 17 Mar 2014 21:13:27 +0000 Subject: Reminder: CCP4 crystallographic summer school in USA, at APS, June 24-July 2 Dear Colleagues, This is a reminder for approaching deadline to apply for the CCP4 Crystallographic Summer School to be held in June at the APS, near Chicago. Please see the original announcement below for more details. We hope to see you at APS in June. With best wishes, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ------------------------------ Dear Colleagues, We are pleased to announce the seventh annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2014/index.php *Title:*"CCP4 crystallographic school: From data collection to structure refinement and beyond" *Dates*: June 24 to July 2. *Site:* Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA *The school content: *Data collection workshop the first two days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is April 11. The application form, the program, contact info and other details can be found at http: http://www.ccp4.ac.uk/schools/APS-2014/index.php<http://www.ccp4.ac.uk/schools/APS-2013/index.php> *Fees: *There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can help make the reservations at economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov __._,_.___ Reply via web post<https://groups.yahoo.com/group/cnsbb/post;_ylc=X3oDMTJwdmJpN3JlBF9TAzk3MzU5…> Reply to sender <[email protected]?subject=Re%3A%20Reminder%3A%20CCP4%20crystallographic%20summer%20school%20in%20USA%2C%20at%20APS%2C%20June%2024-July%202> Reply to group <[email protected]?subject=Re%3A%20Reminder%3A%20CCP4%20crystallographic%20summer%20school%20in%20USA%2C%20at%20APS%2C%20June%2024-July%202> Start a New Topic<https://groups.yahoo.com/group/cnsbb/post;_ylc=X3oDMTJldnZiMm5wBF9TAzk3MzU5…> Messages in this topic<https://groups.yahoo.com/group/cnsbb/message/2257;_ylc=X3oDMTM0dDhrM2VpBF9T…>(1) -------------------------------------------------------- List information at http://groups.yahoo.com/group/cnsbb. Posting is only allowed for members of this list. Visit Your Group<https://groups.yahoo.com/group/cnsbb;_ylc=X3oDMTJlazc1ZTluBF9TAzk3MzU5NzE0B…> [image: Yahoo! Groups]<https://groups.yahoo.com/;_ylc=X3oDMTJkZGZ1bzZpBF9TAzk3NDc2NTkwBGdycElkAzMw…> * Privacy <https://info.yahoo.com/privacy/us/yahoo/groups/details.html> * Unsubscribe <cnsbb-unsubscribe(a)yahoogroups.com?subject=Unsubscribe> * Terms of Use <https://info.yahoo.com/legal/us/yahoo/utos/terms/> . __,_._,___

1 0

MRage run
by Jobichen Chacko 17 Mar '14

17 Mar '14

Dear All, I am running a molecular replacement using MRage program for almost 1 week with 4 threads, but yet to finish the run. I am using Phenix Version dev-1549 I am having a pretty big protein (around 100 KDa). I gave data file, sequence file, one model pdb and output from HHpred as input. Is there anyway to to find out when it is going to finish the run, or I can extract any information from the current run, if I manually end the run? Thank you. Jobi

2 1

phasing high(er) resolution anomalous difference maps with low resolution phases
by Todd Jason Green 13 Mar '14

13 Mar '14

Hello all- I am working on a huge protein assembly(monomer is ~3000 amino acids, large cell ~200, ~200, ~520) that has between 200 and 300 Se-met residues in the asymmetric unit(depending on the number of molecules I pick in the a.u.). I believe I have low resolution phasing from another heavy atom with limits to ~ 6.2 angstrom. Density modified FOMs dip below 0.6 at that point. I can see many tubes that have the diameter of model alpha helices. I ran phenix.find_helices_strands with the helices_before_trace=True option and got a series of helices encompassing about 3400 residues. Assuming that the phasing on the low resolution derivative is true, is it better to use phasing from the lower resolution derivative or phasing from the helical models to fish out the Se-Met sites via an anomalous difference Fourier? I assume I'm stuck at 6.2 for the derivative phasing though i guess i could extend phasing from the map a little further. How far is too far? How high of resolution can I phase from the helices (or from the derivative map for that matter) and still get accurate enough phasing to yield reliable difference peaks to find the Se sites. I have a couple Se-met datasets between 3 and 2.5 angstroms. What sigma levels should I expect for the difference peaks? also, what is the best way to pick the highest difference peaks in the anomalous difference fourier? I didn't see a tool in phenix. "find difference peaks and holes" seems like a logical choice but it seems to want to structure. I've just created maps and used the very old and reliable peakmax in ccp4. I have solved structures like this before but with a lot more info on ncs, envelopes, ncs averaging and a much much smaller protein. I remember getting sites and plugging them into resolve with scripts where you could fix them/or not and phase without looking for more sites, no build etc. Can i just enter sites and phase followed by density modification with one of the gui programs. any comments would be appreciated? and thanks in advance. -Todd

4 3

Postdoctoral position available
by Peter Zwart 11 Mar '14

11 Mar '14

Dear All, The Berkeley Center for Structural Biology at Lawrence Berkeley National Lab is looking for a postdoctoral fellow to work on the development of computational methods aimed at improving the overall quality of crystallographic data and its resulting atomic models. The results of this work will be integrated into the Berkeley Center for Structural Biology (BCSB) crystallography beam lines at the Advanced Light Source. Please have a look at the job posting and contact me for more information: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=77796 Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research 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 SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

1 0

phenix error
by SD Y 04 Mar '14

04 Mar '14

Hi, Could you please tell me why am I getting this error " No atom selected: "name O and chain W and resname HOH and resseq 69". Log file ends as follows: ============================= Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 7 Type Number sf(0) Gaussians Zn2+ 1 27.88 1 S 10 15.96 2 P 2 14.95 2 Mg2+ 3 9.96 1 O 635 7.97 2 N 523 6.97 2 C 1983 5.97 2 sf(0) = scattering factor at diffraction angle 0. ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ======================== Summary of geometry restraints ======================= Number of disulfides: simple=0, symmetry=0 Custom bonds:Sorry------------------------------ Thanks a lotSDY

3 3

project not displayed
by SD Y 03 Mar '14

03 Mar '14

Hi, When I open phenix (1.8.4-1496), I dont see my project. If I import it, it appears. If I close and reopen I disappear again. I have the folders and jobs everything and nothing is lost. Though its not a serious problem, I am wondering if I could get some solution. ThanksSDY

2 1

Rwork/Rfree by resolution shell
by Ursula Schulze-Gahmen 02 Mar '14

02 Mar '14

Where can I found the values for Rwork/Rfree by resolution shell in phenix refinement or analysis. I ran phenix.model_vs_data which provides a list of Rwork by resolution, but no Rfree. Any helpful suggestions? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 642 8766

2 1

fwd: Post-doctoral Fellowship at the University of Texas
by Nathaniel Echols 01 Mar '14

01 Mar '14

---------- Forwarded message ---------- From: "Rudenko, Gabrielle" <garudenk(a)utmb.edu> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Date: Sat, 1 Mar 2014 20:36:00 +0000 Subject: Post-doctoral Fellowship at the University of Texas * Macromolecular Crystallography, Biophysics and Biochemistry* A post-doctoral fellowship position is available at the University of Texas Medical Branch (UTMB) located in the greater Houston area in the research team of Dr. Gabrielle Rudenko. We study molecules that mediate the formation, maintenance and plasticity of synapses, the contact and communication point between neurons. Our proteins of interest organize and regulate protein interaction networks in the synaptic cleft and impact how neurons communicate with each other at synapses. Many of the proteins we study are implicated in neurological disease and serve as potential novel therapeutic targets. We are looking for highly motivated, enthusiastic, hard working individuals who are interested in combining the fields of structural biology and neuroscience. Research projects involve protein over-expression and purification, x-ray crystallography, biochemical and biophysical techniques, proteomics, chemical biology and in collaboration electron microscopy and NMR. Our laboratory is part of the endowed Sealy Center for Structural Biology and Molecular Biophysics and the Department of Pharmacology/Toxicology at UTMB. The Sealy Center provides access to exceptional facilities, training and experimental assistance. *X-ray facilities* include a high-brilliance FR-E Superbright x-ray generator, a Rigaku R-AXIS-IV dual 30cm Imaging Plate detector, a Bruker SMART 2K CCD and a Rigaku BioSAXS-1000 2D-Kratky camera (for solution scattering data). *Biophysics facilities* include equipment for analytical ultracentrifugation, fluorescence, MALDI-TOF mass spectrometry, dynamic light scattering, surface plasmon resonance, titration micro-calorimetry, and high throughput screening with the ThermoFluor HTS apparatus. In addition, the *Electron Microscopy facilities*house three modern JEOL cryo-electron microscopes (a 200 keV JEOL 2200FS cryo-EM with in-column electron energy filter and field emission gun, a 200 keV JEOL 2100 EM, and a 120 keV JEM1400 microscope) and the *NMR facilities*include three NMR spectrometers (Bruker Avance III 800, 750 and 600 MHz with cryoprobes). See http://www.scsb.utmb.edu/resources/ UTMB is part of the Texas Medical Center, the world's largest medical center located in greater Houston. UTMB has research facilities situated on Galveston Island offering a pleasant subtropical climate and miles of relaxing beaches. UTMB is located within commuting distance of Houston, the fourth largest city in the United States and a leader in the arts, education, and health care. *Qualifications:* Applicants should have received a Ph.D. degree in a field relevant to structural biology within in the last three years and have a strong publication record. Applicants with experience in cloning, bacterial/insect cell culture, protein purification and crystallization, and macromolecular structure determination are preferred. However, recent graduates with a strong background in protein over-expression and purification, and an exceptional interest in learning crystallography are also encouraged to apply. Good written and oral communication skills in English are essential as well as the ability and desire to work as part of a highly motivated, collaborative team. To apply please e-mail the following to *rudenkolab.application(a)gmail.com*<rudenkolab.application(a)gmail.com>: CV, contact information for three references (address, phone and e-mail), a list of your experimental expertise and skills relevant to this position and a research statement describing your past research experience and future goals (1-2 pages). Visa sponsorship is available for non-US nationals. For questions, please contact Dr. Gabrielle Rudenko at gabrielle.rudenko(a)utmb.edu For more information please visit http://scsb.utmb.edu/labgroups/rudenko/ The University of Texas is a non-discriminatory, affirmative action employer. Gabrielle Rudenko, PhD Dept of Pharmacology and Toxicology Sealy Center for Structural Biology & Biophysics University of Texas Medical Branch 301 University Boulevard Basic Sciences Building Rm. 5.114B Galveston Texas 77555

1 0

Ligands: a BCSB nano-workshop
by Peter Zwart 28 Feb '14

28 Feb '14

Dear All, On May 2, 2014 the BCSB will be hosting a full day event dedicated to ligands in the life sciences. Access is free, but is limited to 30 participants. The lectures will be streamed allowing remote participation to this event. For onsite and remote attendance, please register to receive further instructions. The registration for on-site participation will be on a first come, first serve basis. The program will cover structural science associated with ligands in the life sciences. Viewpoints from macromolecular crystallography, quantum chemistry, small molecule crystallography and solution scattering will provide the participants with a 360-degree perspective of the role of and technology associated with ligands in structural biology. Please have a look at https://sites.google.com/a/lbl.gov/ligands/home for more information. Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research 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 SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

1 0

observed reflections error?
by Joel Tyndall 28 Feb '14

28 Feb '14

Hi all, I have a minor issue with phenix reporting the number of observed reflections in the output pdb file where it appears to be roughly double (120080 ) to what is actually in an mtz file (~65000) from scala. Any suggestions where this number might originate from? Joel _________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293

4 7

Re: [phenixbb] ERRASER location within rosetta
by Terwilliger, Thomas C 28 Feb '14

28 Feb '14

________________________________ From: Terwilliger, Thomas C Sent: Friday, February 28, 2014 8:42 AM To: Benoît Masquida Cc: Terwilliger, Thomas C Subject: RE: [phenixbb] ERRASER location within rosetta Hi Benoit, I'm sorry for the trouble! The error message, "Sorry, Rosetta version 3.5 or later is needed for ERRASER" is printed if erraser cannot find the file erraser_option.py which should be located in $PHENIX_ROSETTA_PATH/rosetta_tools/ERRASER or $PHENIX_ROSETTA_PATH/tools/ERRASER If you don't have PHENIX_ROSETTA_PATH defined then that would fix it as well. Let me know if this doesn't help! All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Benoît Masquida [b.masquida(a)unistra.fr] Sent: Friday, February 28, 2014 8:27 AM To: PHENIX user mailing list Subject: [phenixbb] ERRASER location within rosetta Hello all, I just built rosetta on my Mac OS 10.8.5 and now try to configure ERRASER within the phenix GUI. I correctly indicated the location of the rosetta build and I specified the same location for ERRASER. However when I start an ERRASER job, an error tells me that "ERRASER works with rosetta3.5 or later version". This is strange because i downloaded one of the latest version of rosetta. I don't know if I gave a wrong locate or if my build is corrupted. Any idea from anyone that could have experienced the same problem? pwd outputs this: /Users/benoit1/share/rosetta_2014wk05_bundle/main, where I find database/ and source/ Thanks. Benoit -- Benoît Masquida Chargé de Recherche CNRS GMGM, UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB, 21, rue René Descartes 67084 Strasbourg b.masquida(a)unistra.fr<mailto:[email protected]>

1 0

ERRASER location within rosetta
by Benoît Masquida 28 Feb '14

28 Feb '14

Hello all, I just built rosetta on my Mac OS 10.8.5 and now try to configure ERRASER within the phenix GUI. I correctly indicated the location of the rosetta build and I specified the same location for ERRASER. However when I start an ERRASER job, an error tells me that "ERRASER works with rosetta3.5 or later version". This is strange because i downloaded one of the latest version of rosetta. I don't know if I gave a wrong locate or if my build is corrupted. Any idea from anyone that could have experienced the same problem? pwd outputs this: /Users/benoit1/share/rosetta_2014wk05_bundle/main, where I find database/ and source/ Thanks. Benoit -- Benoît Masquida Chargé de Recherche CNRS GMGM, UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB, 21, rue René Descartes 67084 Strasbourg b.masquida(a)unistra.fr

1 0

Challenging Refinement at 5 A Resolution
by Erik Walinda 27 Feb '14

27 Feb '14

Dear community, This is my first adventure in crystallography and it seems a rather challenging one. I obtained at dataset at 5.06 A resolution of a 600 residue protein. 3 domains of the protein are already solved by earlier x-ray crystallographic studies. While trying to grow better diffracting crystals and waiting for the next chance to shoot crystals at the synchrotron, I am trying to fit the already solved domains into the electron density of the low data set. Although I tried phaser using the solved structures, I never got a TFZ higher than ~ 6.4. Interestingly, Balbes constructed a model which does not contain any of the already solved domains, but, when using the Balbes output in Phaser, I obtain a TFZ score of 11 and an LLG of 330. (4 molecules / ASU; P2221) If this solution is correct, then in principle it should be possible to fit the already known domains into the structure (I am dreaming of something like a electron-microscopy-type fitting or the early ribosome structures). Phenix refinement however raises the Rfree, instead of lowering it. From my limited knowledge in the field I figured this may be that a) this kind of refinement doesnt work at this resolution or 2) the MR-solution was not really a solution. So I was very excited, when I found the recent papers about DEN refinement and Phenix-Rosetta. I am trying DEN refinement first, using the already solved structures as a reference. The den_refine program nicely creates 2760 DEN restraints. However, after 1 cycle (about 6 h of CPU time at 30 processors), the Rfree goes up (Initial: 0.49; final: 0.57). Indeed, the grid search seems not to be successful, since in the grid search for gamma/w, all Rfree values are rather similar and the lowest Rfree is 0.54. So I would like to ask the community, if ... 1) I shouldn't trust the phaser TFZ score too much and maybe it is just no solution after all? 2) the DEN parameters of phenix.den_refine can be optimized to allow to refine a super-low resolution structure? (I am using the standard parameters from the example: https://www.phenix-online.org/documentation/den_refine.htm) 3) 1 cycle is simply not enough and I should let the computation run for a few days to see, if the Rfree drops down later in the run? 4) Even though Phaser gave me the solution in P2221, may it be that I am trying to refine it in the wrong spacegroup and that's why I fail? Sincerely, Erik

1 0

Re: [phenixbb] unusually high B-factors for selected -heavier- atoms
by Kay Diederichs 27 Feb '14

27 Feb '14

Jan, could it be radiation damage? - that would affect the heavier atoms first/most ... To prove/disprove, use zero-dose extrapolation and re-refine. Kay Am 27.02.14 20:13, schrieb phenixbb-request(a)phenix-online.org: > Date: Thu, 27 Feb 2014 09:50:31 -0800 > From: Jan <jan.abendroth(a)gmail.com> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] unusually high B-factors for selected -heavier- > atoms > Message-ID: <D87628CC-A657-4B4C-B14F-C230C0C2EF00(a)gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > I am refining a pretty high resolution structure (1.65?, P1) with two tetramers of the protein in the ASU using Phenix dev 1630. > Refinement statistics looks really good, R=0.16 Rf=0.18, maps are very clear. However, several sulphur atoms of the protein, and in particular the phosphorous atoms of its cofactor NAD have inflated B-factors, along with distinct FoFc peaks. For instance B-factors for a Met with very well defined density: CB=19.7, CG=27.5, SD=62.2, CE=38.4 > > For some of the residues it is comparable when I refine with or without TLS groups. I used one group per chain of this compact protein, the cofactor is part of each TLS group. Restraints for NAD were generated via eLBOW. When I refine the structure in refmac, using either the standard cif file or the eLBOW generated one, B-factors remain low. > > Any ideas? I am happy to share the data. It is a SSGCID target and will be in the PDB shortly anyway. > > Thanks, > Jan > > > > -- > Jan Abendroth > Emerald BioStructures > Seattle / Bainbridge Island WA, USA > home: Jan.Abendroth_at_gmail.com > work: JAbendroth_at_embios.com > http://www.emeraldbiostructures.com >

1 0

unusually high B-factors for selected -heavier- atoms
by Jan 27 Feb '14

27 Feb '14

Hi all, I am refining a pretty high resolution structure (1.65Å, P1) with two tetramers of the protein in the ASU using Phenix dev 1630. Refinement statistics looks really good, R=0.16 Rf=0.18, maps are very clear. However, several sulphur atoms of the protein, and in particular the phosphorous atoms of its cofactor NAD have inflated B-factors, along with distinct FoFc peaks. For instance B-factors for a Met with very well defined density: CB=19.7, CG=27.5, SD=62.2, CE=38.4 For some of the residues it is comparable when I refine with or without TLS groups. I used one group per chain of this compact protein, the cofactor is part of each TLS group. Restraints for NAD were generated via eLBOW. When I refine the structure in refmac, using either the standard cif file or the eLBOW generated one, B-factors remain low. Any ideas? I am happy to share the data. It is a SSGCID target and will be in the PDB shortly anyway. Thanks, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

3 2

FAQ high res refinement
by Eike Schulz 27 Feb '14

27 Feb '14

> > Dear all, > > I am currently refining a rather well resolved protein at 0.97Å. However, even > after many cycles of refinement the R-factors are stuck at around Rwork/Rfree > 14.5/16.5. Considering number of aa, Rmerge (3.5%) and resolution this seems > to be too high. I assume 10 25 macrocycles should be enough for effective > weight refinement in phenix, however no improvement of the R-factors. > > A quick run with default settings in competitor software 'R' yields >2% better > R-factors. > > I would appreciate suggestion how to improve my refinement protocol, values > differing from default are listed below. > > Thank you very much in advance > > Eike > > > > > > > refine { > adp { > individual { > isotropic = element H > anisotropic = not element H > } > group_adp_refinement_mode = one_adp_group_per_residue \ > *two_adp_groups_per_residue group_selection > } > } > main { > apply_overall_isotropic_scale_to_adp = False > nqh_flips = False > ordered_solvent = True > place_ions = True > number_of_macro_cycles = 10 > hydrogen_bonds = True > use_convergence_test = True > target = auto *ml mlhl ml_sad ls > random_seed = 3326496 > wavelength = 0.885611 > nproc = 4 > } > hydrogens { > refine = individual *riding Auto > } > tls { > find_automatically = False > one_residue_one_group = False > } > ordered_solvent { > mode = second_half filter_only every_macro_cycle \ > *every_macro_cycle_after_first > h_bond_min_mac = 1 > h_bond_min_sol = 1 > h_bond_max = 6 > refine_occupancies = True > new_solvent = isotropic *anisotropic > b_iso_min = 0 > } > peak_search { > max_number_of_peaks = 1303 > } > target_weights { > optimize_xyz_weight = True > optimize_adp_weight = True > wxc_scale = 0.2 > wxu_scale = 0.2

2 1

Option for renumber the pdb
by Rojan Shrestha 27 Feb '14

27 Feb '14

Hello, I have found the program phenix.pdbtools. Maybe, it can renumber residues of pdb. I have found the options renumber_residues options but I am unable to see the options for starting residues. I have pdb starts from 1 and want to renumber 1 into 250. Can somebody tell me how to put the option for starting residue? Regards, Rojan

5 5

scaling in phenix.fobs_minus_fobs_map
by Michael Thompson 27 Feb '14

27 Feb '14

Hello, I have a very simple question about phenix.fobs_minus_fobs_map, and it's implementation in the GUI. I just want to make sure I am not skipping an important step in generating my isomorphous difference map. I'm trying to create an Fo-Fo map for two data sets at pretty different resolutions, using phases from a model. I truncated the higher-res data so the high resolution limit matches the lower-res data set. Are these 2 mtz files sufficient for input into phenix.fobs_minus_fobs_map, or do I need to use another utility to scale the two data sets together prior to calculating the map coefficients? I suppose another way to ask my question would be, does phenix.fobs_minus_fobs_map perform scaling of the two Fobs arrays before calculating the new map? Thanks for clarifying, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

2 1

problem phenix ensemble
by Firas FADEL 25 Feb '14

25 Feb '14

Hello, I am using phenix ensemble to refine an X-ray structure of a protein (40kDa) at 1.05 A in complex with a ligand. The occupancy of the ligand is 73%. After refining the structure, I found out that the program confused the position of the ligand and put some water molecules. Do you have any suggestion or a command to avoid this problem. If you need details I can send you the mtz and pdb files. Thanks in advance. Firas Fadel Firas FADEL Institut de Génétique et de Biologie Moléculaire et Cellulaire, IGBMC Equipe Alberto PODJARNY, 1 Rue Laurent Fries, 67404 Illkirch-France Email : fadel(a)igbmc.fr<mailto:[email protected]> Tel: + 33 (0) 3 88 65 33 13<tel:%2B%2033%20%280%29%203%2088%2065%2033%2013>

1 0

Announcement: QuantumBio Release of QM-based X-ray Crystallography Plugin v1.0 for Phenix
by Lance Westerhoff 25 Feb '14

25 Feb '14

Hello All- We are pleased to announce the release of our linear scaling, quantum mechanics DivCon Discovery Suite plug-in v1.0 for the Phenix, x-ray crystallography platform. As was detailed in the recent Phenix Newsletter, when this plugin is installed, the conventional refinement functional along with the stereochemical restraints or CIFile for the ligand(s) and for the surrounding active site(s) are replaced with QM data in "real time" during the refinement in order to increase structural accuracy and decrease artificial strain. To see the full press release along with references and links for further information, please take a look at the following website: http://www.quantumbioinc.com/news/show/PhenixAnnouncement To encourage adoption, we have waived the license fee for non-profit, academic use and we have posted our commercial evaluation license as well. These licenses are available at the following link: http://www.quantumbioinc.com/products/software_licensing Certainly, let me know if you have any questions or if you would like to try out the technology on your own structures. -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com

1 0

revisiting "Problem with loop fitting "
by Alejandro Buschiazzo 24 Feb '14

24 Feb '14

Dear phenix community I am attempting to use phenix.fit_loops for the first time and getting an error message: "No suitable gap found matching residues" I found a short exchange exactly about this (Jan 2011), but eventually Tom Terwilliger asked for the files directly to see if he could solve it. I can't seem to find a later summary of the solution. (apparently, the most probable reason was some kind of mismatch between PDB numbering and sequence file...which I shouldn't have... I'm probably missing some silly here - I have been fiddling around with the sequence file in many ways...with no success) many thanks for any help! alejandro -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

2 4