- phenixbb - phenix-online.org

Re: [phenixbb] elbow
by Mengbin Chen 13 Jun '13

13 Jun '13

Dear Dr. Dias, I tried the command line in Terminal, but Elbow still regularized the conformation and bonds of the ligand and the result turned out to be the same with that I ran thorough GUI. The thing is that the input pdb file has a conformation the ligand should adopt so that I do not really want energy minimization or geometry optimization to be done on it. Although I set "none" for "geometry optimization" in GUI, it unfortunately changed the ligand conformation. Thank you, Mengbin On Thu, Jun 13, 2013 at 2:52 PM, Mengbin Chen <mengbinc(a)sas.upenn.edu>wrote: > Dear Dr. Dias, > > I tried the command line in Terminal, but Elbow still regularized the > conformation and bonds of the ligand and the result turned out to be the > same with that I ran thorough GUI. The thing is that the input pdb file has > a conformation the ligand should adopt so that I do not really want energy > minimization or geometry optimization to be done on it. Although I set > "none" for "geometry optimization" in GUI, it unfortunately changed the > ligand conformation. > > Thank you, > Mengbin > > > On Thu, Jun 13, 2013 at 2:42 PM, Joao Dias <joao.dias(a)heptares.com> wrote: > >> Dear Mengbin, >> You can open a terminal window and run elbow as a command line. >> >> phenix.elbow --final_geometry input_file.pdb**** >> >> >> Do not forget to initialize the phenix environment, depending on your >> terminal shell, one example is: >> source >> /Applications/PHENIX-dev-1320/Contents/phenix-dev-1320/phenix_env.sh >> >> All the best, >> Joao >> >> Dr Joao Dias**** >> >> Principal Scientist**** >> >> ** ** >> >> Heptares Therapeutics Ltd**** >> >> BioPark, Broadwater Road,**** >> >> Welwyn Garden City,**** >> >> Herts, AL7 3AX**** >> >> UK >> >> From: Mengbin Chen <mengbinc(a)sas.upenn.edu> >> Reply-To: PHENIX user mailing list <phenixbb(a)phenix-online.org> >> Date: Thursday, 13 June 2013 19:32 >> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> >> Subject: [phenixbb] elbow >> >> Dear PHENIX Users, >> >> I have been playing around with Elbow for a while, but I kept having >> problems generating .cif file. For "Chemical file type" and "Template PDB >> file", I used the pdb file of the ligand. Since the coordinates in the pdb >> file corresponds to a conformation desired, I chose "None" for "geometry >> optimization". After running Elbow, the output pdb file was completely >> different than the input one -- even double bonds became single bonds and >> 10-membered ring conformation changed. I have tried Sketcher in CCP4 >> package, but no good results either. Could anyone tell me how to do this >> correctly? Any help is appreciated! >> >> Thank you in advance, >> Mengbin >> >> -- >> Mengbin Chen >> Department of Chemistry >> University of Pennsylvania >> >> [image: www.heptares.com] <http://www.heptares.com><http://www.heptares.com> >> >> >> The information in this e-mail is confidential and may be legally >> privileged. It is intended for the exclusive attention of the addressee >> stated above and should not be copied or disclosed to any other. If you >> have received this transmission in error, please make no use of its >> contents and contact the sender. Contact and registered office address: >> Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden >> City, Hertfordshire, AL7 3AX. Company No: 06267989 >> >> > > > -- > Mengbin Chen > Department of Chemistry > University of Pennsylvania > -- Mengbin Chen Department of Chemistry University of Pennsylvania

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elbow
by Mengbin Chen 13 Jun '13

13 Jun '13

Dear PHENIX Users, I have been playing around with Elbow for a while, but I kept having problems generating .cif file. For "Chemical file type" and "Template PDB file", I used the pdb file of the ligand. Since the coordinates in the pdb file corresponds to a conformation desired, I chose "None" for "geometry optimization". After running Elbow, the output pdb file was completely different than the input one -- even double bonds became single bonds and 10-membered ring conformation changed. I have tried Sketcher in CCP4 package, but no good results either. Could anyone tell me how to do this correctly? Any help is appreciated! Thank you in advance, Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

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Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"
by Sam Stampfer 12 Jun '13

12 Jun '13

Dear Phenix Community, I am preparing my structure for deposition and ran it through the Generate "Table 1" function in phenix. The inputs I gave it were my .mtz structure factors file, the final pdb coordinate file, and the log file from hkl2000. I did not provide unmerged data. My pdb file (which had been refined using phenix.refine) had values of r_work=0.2342 r_free=0.2603 However, phenix.model_vs_data (from Generate "Table 1") gave me r_work=0.2940 r_free=0.3150 I also got this warning about resolution limits, but I think it should not have affected the R-free calculation to this extent: WARNING: Resolution limits in scaling log for structure A549T are inconsistent with resolution limits in the MTZ file: 50.00 - 3.02 (in logfile) 48.47 - 3.03 (in MTZ file) When I refined my model in phenix, I used the twin law h,-h-k,-l. I read in the documentation that twinning can account for some of this discrepancy, but that the program is supposed to take twinning into account if it will lower the calculated R-work by more than 2%, which it doesn't seem to have done (or there is some other problem with my data). Thanks for your help! -Sam

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den refinement
by Andreas Förster 12 Jun '13

12 Jun '13

Dear all, I'm trying to get DEN refinement going from the command line. The run aborts quickly with the following error in the log file: Sorry: Cartesian simulated annealing should not be turned on for DEN refinement. Annealing settings are controlled in the den parameter scope. The DEN scope in input.def looks like this: den { reference_file = den_ref_Jun.pdb gamma = 0.5 kappa = 0.1 weight = 30 sigma = 0.44 optimize = True opt_gamma_values = 0 0.2 0.4 0.6 0.8 1 opt_weight_values = 3 10 30 100 300 num_cycles = 12 kappa_burn_in_cycles = 2 bulk_solvent_and_scale = True refine_adp = True final_refinement_cycle = False verbose = False annealing_type = *torsion cartesian output_kinemage = False restraint_network { lower_distance_cutoff = 3 upper_distance_cutoff = 15 sequence_separation_low = 0 sequence_separation_limit = 10 exclude_hydrogens = True ndistance_ratio = 1 export_den_pairs = False den_network_file = None } Annealing type is torsion from what I can tell. What am I doing wrong? (Release tag: 1394, Platform: intel-linux-2.6-x86_64 redhat-e6.2) Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

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Discrepancy between phenix.refine and phenix.model_vs_data R-factors
by Abhinav Kumar 11 Jun '13

11 Jun '13

I am getting a significant difference between the R-factors written by phenix.refine and phenix.model_vs_data. 1. Phenix.refine phenix.refine "in.pdb" "Fobs.mtz" "refinement.input.xray_data.labels=FP SIGFP" "refinement.input.xray_data.high_resolution=2.50" "fix_rotamers=True" "ordered_solvent=True" "strategy=tls+individual_sites+individual_adp" Final R-work = 0.1829, R-free = 0.2141 2. Phenix.model_vs_data phenix.model_vs_data out.pdb Fobs.mtz f_obs_label="FP" r_free_flags_label="FreeR_flag" high_resolution=2.50 comprehensive=true r_work(re-computed) : 0.1808 r_free(re-computed) : 0.2099 How can I reproduce the phenix.refine R-factors in phenix.model_vs_data? -- Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992

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phenix elbow: is similar compound helpful to create restraint for new ligand?
by Rongjin 11 Jun '13

11 Jun '13

Hello Phenix users, I have tetrabutylphosphonium in my crystal. I found a similar compound tetrabutylammonium (PDB residue name TBA) which are found in several PDB entries. Usually I draw the new compound in 2-D format and convert to 3D and then create restrain files. In this case, considering N and P are very similar, will the TBS be helpful for elbow to generate restrains for tetrabutylphosphonium? Thanks Rongjin Guan

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Hi
by Wei Shi 10 Jun '13

10 Jun '13

Hi all, I was trying to solve the structure of a protein in several different datasets using xds and phenix. I could solve the structure from one dataset in space group P4. For another dataset, I could solve the structure using the monomer of the structure I got from the first dataset as search model and solve the structure in space group mC. For the third dataset, in IDXREF.LP, the space group of the highest symmetry is hp: 101.2, 101.3, 58.8, 90, 90, 120. According to Mathiews coefficient, 1 monomer is expected in the asymmetric unit. But I couldn't get the molecular replacement solution using the same method as for the second dataset. I also tried several other search models (eg. deletion of the potential flexible region in the search model) and tried to find the solution in all possible pointgroup. I also tried to process the data in oC (C222), the space group of the second highest symmetry in IDXREF.LP, but, still I could not get right molecular replacement solution. I don't whether this means that there is a big conformational change for the structure in the third dataset or the space group I use is not right. Let me know if any of you would have any comments or suggestions for me. Thank you so much! Best, Wei

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Postdoc Position - Berkeley
by Paul Adams 07 Jun '13

07 Jun '13

Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 76029 Division: Physical Biosciences (Joint BioEnergy Institute) Date Opened: 6/5/2013 Summary: A postdoctoral position is available at the Joint BioEnergy Institute in Emeryville to work on proteins involved in plant cell wall synthesis. To learn more about JBEI visit: http://www.jbei.org/ Duties: Implementation of methods for the cloning, protein expression, and purification for glycosyl transferases, typically using the Gateway system for gene manipulation. Transformation of host organisms for protein expression, followed by assay of protein expression, and scale up of expression and sample processing (such as deglycosylation). Purification of proteins for biochemical and structural studies. Expression in multiple systems, including E. coli, yeast and insect cells. Qualifications: a Ph.D. in biochemistry, molecular biology, structural biology, or a related field. Demonstrated experience with protein expression, especially in systems other than E. coli. First-author publications demonstrating prior results in the area of protein expression. Experience with cloning methods and protein purification methods. Strong problem solving skills. Solid interpersonal skills and the ability to work in a team environment are critical. Experience with the practical aspects of structure solution by X-ray crystallography would be helpful but not essential. Note that this is a multi-year position that is renewed annually on the basis on performance and continued funding. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years, and 57 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. To apply visit https://lbl.taleo.net/careersection/2/jobsearch.ftl?lang=en and search for the job number 76029 or visit: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=76029 -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area 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. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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From Dmitri Svergun and Matthias Wilmanns: BSR-2013: Abstract submission deadline is extended until 20th June!
by Terwilliger, Thomas C 07 Jun '13

07 Jun '13

11th International Conference: Biology and Synchrotron Radiation (BSR), 8-11 September 2013, EMBL Hamburg, Germany The abstract submission deadline for BSR-2013 is extended until Thursday 20th June, 2013! Biologists, physicists, chemists, from students to principal investigators, are invited to this tri-annual meeting with rich traditions. Do not miss the unique opportunity to present your work, meet colleagues, friends and future collaboration partners from all over the world. Check out our preliminary programme to learn more. BSR 2013 offers a tour of DESY’s most impressive research infrastructures and includes a broad social programme to discover the vibrant city of Hamburg. Accompanying persons will enjoy special rates! Extended deadlines: ·Registration and abstract submission: 20 June 2013 ·Registration without abstract: 15 August 2013 Take a look at the updates BSR webpage ( www.bsr2013.org<http://www.bsr2013.org/>) for more information and to register. CONTACT: Diah.Yulianti(a)embl.de<mailto:[email protected]>, or margret.fischer(a)embl-hamburg.de<mailto:[email protected]> Alternatively, contact us on the event facebook page

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Re: [phenixbb] Pseudotranslation issue
by Gino Cingolani 07 Jun '13

07 Jun '13

Dear Fulvio, We just had a similar problem (further complicated by some twinning). Assuming that: 1. You collected enough data and 2. You don't have a crazy number of molecules in the tetragonal asymmetric unit, I would advice to scale your data in P1 and do MR in P1. Then use conventional refinement + model building to bootstrap a better model (most likely your initial model isn't as good). Rosetta may help, too. Then eventually go back to the tetragonal data with the improved search model and see if LLG and packing make sense. Gino **************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu Website: http://www.cingolanilab.org **************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) Fulvio Saccoccia <fulvio.saccoccia(a)uniroma1.it> wrote: >Dear phenixbb, > I have a data set collected at 2.2A resolution that I can integrate >in P4. Aimless, Phaser and Xtriage recognized a pseudotranslation >(34.6% of origin peak) at fractional coordinates 0.500 0.500 0.479 >(ORTH 46.7 46.7 37.4). However labelit.index run with >sublattice_allow=true search did not detect the pseudotranslation >vector. So far, any attempts to phase by molecular replacement was >unsuccesfull and I suspect that it could be due to incorrect assignement >of space group: > >Now, some questions arise: >1) does the pseudo translation exist or do not? >2) if translational NCS is present, could it mimic a P41/P42/P43 space >group? >3) in any case, any advices in order to properly deal with tNCS will be >of great help? > >I thank you in advance >Best wishes > >-- >Fulvio Saccoccia, PhD >Sapienza University of Rome >Dept. of Biochemical Sciences "A. Rossi Fanelli" >Piazzale Aldo Moro, 5 >00185 Rome (Italy) > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://phenix-online.org/mailman/listinfo/phenixbb > The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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