- phenixbb - phenix-online.org

Several postdoc opportunities, Shanghai University
by Pavel Afonine 18 May '15

18 May '15

Posted on behalf of Prof. Ren Wei and Jeffrey Reimers. **************************** *Post-Doctoral Fellowships in Quantum Refinement of Protein X-ray Crystallographic Structures and related work in Biophysics, Biochemistry, Biomaterials, Chemistry, and Soft Condensed Matter*** Shanghai University (http://www.shu.edu.cn) isseeking multiple outstanding postdoctoral researchers to be part of the newly created International Centre for Quantum and Molecular Structure (ICQMS). Parallel Adjoint Appointments at The University of Technology, Sydney (UTS) (http://www.uts.edu.au/about/faculty-science/physics-and-advanced-materials), Department of Mathematical and Physical Sciences, will also be available. Most available positions relate to the core project of ICQMS: the development of codes for automatic quantum refinement of protein crystallographic structures. For these positions, previous experience at the PhD or post-doctoral level in the simulation of protein structure is essential. This could involve mastering of quantum-chemical software, molecular dynamics methods, statistical mechanics theories, or protein structure refinement. Positions are available for both software users and methods developers. ICQMS also has a wider view, considering the determination of protein function and spectroscopy, especially for photosynthetic proteins, understanding the effects of solvation and environment on molecular properties, quantum dynamics and coherence in proteins, understanding order/disorder transitions, the fundamental role played by entropy in controlling protein structure, the properties of biomaterials such as cement, general self-assembly processes such as organic self-assembled monolayer formation and properties, and the properties of bulk materials. A position is also available concerning the development and application for GPUs of Hartree-Fock theory or Density-Functional Theory or molecular dynamics. All positions require a PhD in Chemical Physics, Quantum Chemistry, Computational Biochemistry, Crystallography, or related disciplines. Excellent verbal and written communication skills in English are essential. Proven independence is also essential. Candidates that have contributed to scientific-community activities and/or teaching innovation will be considered favourably, as will those that have contributed independently to multidisciplinary team projects. Shanghai University is a well funded, internationally connected, rapidly raising University with a strong profile in Material Science, and indeed under the direction of University President Prof. H. J. Luo is a central player in the extensive Chinese Materials Genome Initiative (MGI) Project. ICQMS extends this vision into mainstream chemical and biochemical research. Adjunct Appointments at the University of Technology Sydney will allow each Postdoctoral Fellow to spend 6 months doing joint research in Sydney with UTS staff. Shanghai University and The University of Technology Sydney have a 20-year history of close collaboration, including the joint Smart Cities Institute and the Sydney Institute of Language and Commerce. This collaboration also includes the dual PhD degree program between the two universities. The negotiable anticipated start date is 2015 between August and December. The positions are available for two years and renewable subject to a performance review. Shanghai University is an Equal Opportunity Employer and all persons are encouraged to apply. Applicants should send their curriculum vitae including lists of publications, summaries of their research interests, lists of prizes and awards, summaries of any teaching, community service or administrative experience, and have three reference letters sent directly to yarulove2006(a)shu.edu.cn <mailto:[email protected]>. Further information can be obtained from: ICQMS Director: Jeffrey Reimers reimers(a)shu.edu.cn <mailto:[email protected]> or ICQMS Deputy Director: Wei REN renwei(a)shu.edu.cn <mailto:[email protected]> Closing Date: 2015 December 31^st , or until all positions are filled.

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Submissions for Comput. Cryst. Newsletter
by Nigel Moriarty 14 May '15

14 May '15

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the July 2015 issue is 15 June 2015. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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how to generate an isomorphous difference map
by crystallogrphy 13 May '15

13 May '15

Hi, I am trying to generate an isomorphous difference map with phenix GUI. I input reflection 1 and 2 with mtz format and a PDB model, I got an MTZ format map file. Because I want to load it to coot or pymol with negative and positive density, I need to transform this mtz map to ccp4 map. However, FFT map cannot work. Does any know how can I get a ccp4 format maps with positive or negative density? Thanks!

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Scientist-I (Structural Biology) - Frederick National Lab for Cancer Research
by Dhirendra K Simanshu 13 May '15

13 May '15

Dear colleagues, We have an opening for a Scientist-I (Structural Biology) position here in Frederick, MD. If not interested, please forward this email to those who might be. To apply for this position and for further details, including a job description and qualifications, please click on the link below: http://jobs.leidos.com/ShowJob/Id/475028/Scientist-I-615658-%28NCI%29/ Thank you Dhirendra *------* *JOB DESCRIPTION * The Scientist I will work in support of the FNL/NCI RAS Initiative. One of the major objectives of the RAS initiative at the Frederick National Lab for Cancer Research (FNLCR) is to conduct structural analysis of KRAS mutants and biologically relevant KRAS activator/effector complexes in support of drug discovery efforts. The Scientist I will be responsible for: 1) carrying out structural studies on KRAS-effector complexes through the entire protein crystallographic process, including construct design, protein purification, biochemical and biophysical characterization, crystallization, X-ray data collection, structure determination and analysis, 2) working closely with an integrated team of protein scientists in the Protein Expression Laboratory (PEL) at the FNLCR, 3) participating in experimental design and to independently conduct experiments in a priority-driven environment, 4) completing projects independently and as part of a team, and providing timely updates of the project progress to their supervisor both informally and by formal report writing, and 5) generating high-quality peer-reviewed publications. Work may involve the use of potentially hazardous chemical, biological, or radiological materials or may be located in areas where such materials are used. May require the use of personal protective equipment and adherence to strict safety protocols. *Qualifications:* *BASIC QUALIFICATIONS* - PhD in structural biology, protein biochemistry, crystallography, or in a related discipline from an accredited college or university appropriate to biomedical research, or eight (8) years’ experience in lieu of degree - Foreign degrees must be evaluated for U.S. Equivalency - In addition to the educational requirements the candidate will need proven ability in all aspects of protein crystallography from construct design through structure determination and interpretation - Extensive experience in crystallization of protein-ligand and protein-protein complexes - Experience collecting data at synchrotron beamline and solving ab initio structures - Expertise in commonly used crystallography software packages - Proficiency in protein biochemical and biophysical characterization - Record of publications in peer-reviewed journals *PREFERRED QUALIFICATIONS* - Relevant postdoctoral experience in a structural biology laboratory. - Experience working with small GTPases, RAS-related activator/effector proteins, or membrane-associated complexes. - Knowledge of molecular dynamics simulations and protein-ligand docking. *To apply*, click here: http://jobs.leidos.com/ShowJob/Id/475028/Scientist-I-615658-%28NCI%29/

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on minimization_global of phenix.real_space_refine
by Smith Liu 13 May '15

13 May '15

Dear All, For minimization_global of phenix.real_space_refine, does it has relationship with the input map, or it is only processed based on the input pdb? Smith

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Re: [phenixbb] how to generate an isomorphous difference map
by Edward A. Berry 12 May '15

12 May '15

OK. Knowing that and rereading the OP's question and your reply, I think that was the right answer. Apologies to CCP4 for accidentally cross-posting. eab On 05/12/2015 01:21 PM, Philip Kiser wrote: > There is a tool within PHENIX that prepares an mtz file for generation of an isomorphous difference map (scales the two datasets together, etc). I assumed that is what the OP was talking about. > > On Tue, May 12, 2015 at 12:54 PM, Edward A. Berry <BerryE(a)upstate.edu <mailto:[email protected]>> wrote: > > OK. I guess I was thinking of subtracting 2fo-Fc maps, which would give essentially (Fo1-Fo2) coefficients. But coming out of phenix it will be at least 2mFo-DFc, with different m's and D's for the two datasets. Makes it rather more complicated. > eab > > On 05/12/2015 11:58 AM, Philip Kiser wrote: > > Good points. But also, the traditional isomorphous difference map is not as susceptible to model bias issues compared to a real space difference map (or a "vector" isomorphous difference map). > > On Tue, May 12, 2015 at 11:37 AM, Edward A. Berry <BerryE(a)upstate.edu <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: > > > > On 05/12/2015 09:46 AM, Philip Kiser wrote: > > crystallogrphy, > > If you did everything correctly, you should be able to directly calculate the difference map in Coot from the MTZ file generated by PHENIX. You would need to open it with "Open MTZ" rather than "Auto open MTZ" and then select the appropriate map coefficients. Note that what Tim described (a real space difference map) is technically different from the traditional isomorphous difference map where the SF amplitudes of the two data sets are subtracted prior to the map calculation. > > Philip > > > Should be the same, due to linear property of the Fourier transform, EXCEPT for possible scaling differences and treatment of missing data. This latter could be significant, since presumably the traditional methods omits reflections unless present in both datasets, whereas in Tim's method each map will be made with all data available in that dataset. As a result, the largest coefficients in Tim's difference map might be the reflections which are absent in one map and present in the other. But if both have good completeness, it may not matter. > > eab > > > > On Tue, May 12, 2015 at 9:24 AM, Tim Gruene <tg(a)shelx.uni-ac.gwdg.de <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>>> wrote: > > Dear crystallogrphy, > > you can open the PDB file with Coot, then use File -> Open MTZ to read one > mtz-file after the other into Coot. Coot will offer to generate the map > coefficients from the previously loaded PDB file. > > Once you have both maps, you can go to Extensions -> Maps -> Make a Difference > Map to create the difference map. > > In order to see both positive and negative density, you choose Extensions -> > Maps -> Set Map is a Difference Map. > > Regards, > Tim > > On Tue, May 12, 2015 at 08:43:45PM +0800, crystallogrphy wrote: > > Hi, > > > > I am trying to generate an isomorphous difference map with phenix GUI. I > > input reflection 1 and 2 with mtz format and a PDB model, I got an MTZ > > format map file. Because I want to load it to coot or pymol with negative > > and positive density, I need to transform this mtz map to ccp4 map. > > However, FFT map cannot work. > > Does any know how can I get a ccp4 format maps with positive or negative > > density? > > > > Thanks! > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> > > http://phenix-online.org/mailman/listinfo/phenixbb > > Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> > > > -- > -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > phone: +49 (0)551 39 22149 <tel:%2B49%20%280%29551%2039%2022149> <tel:%2B49%20%280%29551%2039%2022149> <tel:%2B49%20%280%29551%2039%2022149> > > GPG Key ID = A46BEE1A > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> > > >

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Postdoc Position - Berkeley, California
by Paul Adams 10 May '15

10 May '15

Lawrence Berkeley Laboratory Postdoctoral Fellow Job ID: 80929 Division: Physical Biosciences Date Opened: 5/8/2015 Summary: A postdoctoral position is available to work on developing new methods for macromolecular structure determination and refinement with the PHENIX software system. To learn more about Phenix visit: http://www.phenix-online.org Duties: Development and implementation of computational algorithms for structure determination using crystallography. Including methods for the assessment of crystallographic data quality, improved methods for minimization of target functions, algorithms for the automated parameterization of structure refinement, new target functions for the refinement of structures, and enhanced structure deposition tools. Qualifications: Ph.D., or equivalent experience, in computational crystallography, computational biology, bioinformatics, computational chemistry or a related field. Demonstrated experience with computational methods development. Publications in macromolecular crystallography or related field. Familiarity with software development tools such as C++, C and scripting languages such as Python. Good programming and mathematical skills. Solid interpersonal skills and the ability to work in a team environment are important. Ability to communicate with a broad range of researchers. 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 80929 or visit: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=80929 -- 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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Molecular replacement at low resolution
by mohamed noor 09 May '15

09 May '15

Dear developers I have a dataset to about 4 A in point group P 4 2 2 (Pointless suggests P 41 21 2). The protein is about 11 kDa and has an identity of about 50 % to my search model. Phaser calculated the eLLG to be about 5, and maybe not surprisingly, it failed even after using Sculptor to prepare the model. It also says that solutions with Z-scores more than 8 were rejected for failing the packing test. Are there any suggestions on getting a solution? Solvent content calculation from Xtriage suggests about 8 copies in the asu. Would this be of any help in MR? Thanks.

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Raw diffraction images required
by mohamed noor 09 May '15

09 May '15

Dear all I am looking for diffraction images that were collected to a resolution of 3 A or so (by visual inspection), highly redundant and the I/sigma at the outermost resolution should be low (not more than 1). Maybe there is something already in the JCSG database but I don't know exactly which one. I want to show that high redundancy can provide a background average to extract weak but useful spots and that this relationship increases to a certain limit. Thanks.

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How to fix atoms in refinement
by Rajeshwer Sankhala 07 May '15

07 May '15

Hi, I have flexible a flexible loop in my structure and every time i refine it derange ramachandrans. Can anyone suggest how can i fix these flexible residues in phenix refinement so basically i don't wanna refine them. Can i do this in GUI? Thanks Raj 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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feature request: update project
by Sebastiano Pasqualato 07 May '15

07 May '15

Dear Phenix developers, it happened to me recently to go from one Mac to another, working on the same Phenix projects. I have the directory synchronised via Google Drive, with the same absolute path. Importing a project is not a problem, at all. The problem is that, if I modify one project on one computer, the changes are not “seen” by the other computer, and there is no way to “update” the project, forcing it to read the info on the .phenix directory. Would that be difficult to implement? Thanks a lot in advance, best, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit <http://is.gd/IEO_XtalUnit>

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on phenix.real_space_refine
by Smith Liu 06 May '15

06 May '15

Dear All, If I only want to refine resi 30-50 in Chain A by phenix.real_space_refine, and my protein contains A, B, C chains of a identical sequence of 800 aas, will you please let me know how can I specify "residue 30-50 of Chain A" in the phenix.real_space_refine command? Smith

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neutron refinement of protonated Glu and residues with alternate conformation
by crystallogrphy 05 May '15

05 May '15

Hi, I am doing joint X-ray and neutron refinement for my structure. I found a few residues with two alternate conformations. After I generated alternation conformations, I used phenix.readyset to generate hydrogen and deuterium atoms for D/H atoms. However, phenix.readyset only gives H atoms for exchangable H atoms, such as the amide H atoms. The reason is that A and B letters have been assigned for the alternate conformation, not for the D/H atoms for particular conformations. Could anyone know how to solve this problem? The second question is that I found one Glu residue is protonated at OE1 atom of its carboxylate side chain. How could I generate protonated Glu? Do I need a strain file for this? Thanks! Qun

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SA
by Irina PROKHOROVA 01 May '15

01 May '15

Hello, I am trying to run coordinate refinement 5 cycles with first cycle of simulated annealing (torsion) via command line. Here is a part of my params file that I adapted from my colleges: refinement.main { number_of_macro_cycles = 5 target = *ml mlhl ml_sad ls simulated_annealing_torsion = True } simulated_annealing { mode = every_macro_cycle second_and_before_last once *first first_half } refinement.refine { strategy = *individual_sites individual_sites_real_space rigid_body \ individual_adp group_adp tls occupancies group_anomalous sites { individual = segid *A individual = segid *B } As a result I get the Error Unused parameter definitions: simulated_annealing.mode (file "refine.params", line 26) Could you help me with the syntax, please. Should I include sites definition for simulated annealing? Irina

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Phenix.real_space_refine and B-factor
by Smith Liu 30 Apr '15

30 Apr '15

Dear All, By Phenix.real_space_refine if is very nic to fit a PDB into an EM map, and we can get a fitted PDB. However no matter what is the run strategy (default, morphing, local grid search, etc), in the got PDB the B-factors for each atom in the coordinates were always those from the original input PDB, which may make the B-factors in refined PDB meaningless. As finally we need to deposit the refined PDB and EM to the database, will you please explain how to settle the B-factor issues in the refined PDB related to Phenix.real_space_refine? Smith

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on B-factor refine
by Smith Liu 29 Apr '15

29 Apr '15

Dear All， If in the Phenix refine GUI, I only want to refine based on individual B-factors, can I only click "individual B-factors" without cliking any other items in the "Strategy" and without clicking any items in the "Targets and weighting" and "other options"? Further, if I only click "XYZ cordinates" without cliking any other items in the "Strategy" and without clicking any items in the "Targets and weighting" and "other options", what the Phenix refine realy do? Smith

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extra density for phosphorylated Thr
by Ursula Schulze-Gahmen 29 Apr '15

29 Apr '15

I have a structure with a phosphorylated Thr (TPO). As far as I can see, phenix recognizes the TPO residue, but the electron density maps have a large positive density around the side chain of this residue. Any suggestion what is wrong? Do I need a special definition file for the TPO? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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Number of reflections
by Ana Ramos 29 Apr '15

29 Apr '15

Dear all, I am finishing with the refinement of my structure and I noticed that the number of observed reflections used for refinement 36720 is less than 80 percent of observed reflections for data collection (172551). I am aware that the data collection statistics should be calculated in the same resolution range of refinement. Do you know the reason of this difference? I just followed the instructions from HKL where I indexed and scaled and then used Phenix for MR and refinement. Ana

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on phenix.real_space_refine
by Smith Liu 29 Apr '15

29 Apr '15

Dear All, If with phenix.real_space_refine, I got a model (with PDB), in which there is a fragment containing several residues (not in continuation in the fragment), with side chains not fitting to the corresponding side chain density (or out of the density, but close to the density), which function(s) of phenix.real_space_refine (for example,minimization_global or local_grid_search?) can improve the fitting of the sidechains to the density? I am looking forward to getting your reply. Smith

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Autobuild on parallel
by Kaushik Hatti 29 Apr '15

29 Apr '15

Hi, What is the best way to run Autobuild if I need to run it on hundreds of datasets (through command-line)? I have a single machine with 24 cores and access to a cluster with 128 cores (on parallel; accessible only through PBS script). Each Autobuild job with nproc=4 on a single core machine takes ~12 hours to run (nproc > 4 wouldn't make any difference in the speed of computation?!). However, I read that I could set nproc=10 (or more) and run on parallel ( https://www.phenix-online.org/documentation/reference/autobuild.html#parall…). When I tried the same through PBS script, I got the following error, XXXXXXXXXXXXXX Running up to 1 jobs in parallel... with total of 3 jobs Splitting work into 3 jobs and running with 1 processors using qsub background=False nproc=20 background=False in ~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0 Final job will be run with sh with background=True Starting job 1...Log will be: ~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0/RUN_FILE_1.log Traceback (most recent call last): File "~opt/phenix-1.9-1692/phenix/phenix/autosol/AutoBaseExtend.py", line 989, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "~opt/phenix-1.9-1692/phenix/phenix/autosol/AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 2364, in AutoBuild_build_cycle self.AutoBuild_rebuild_cycle_run() File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 4647, in AutoBuild_rebuild_cycle_run always_reuse_model=always_reuse_model) File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 7452, in AutoBuild_build_refine mtz_file=mtz_file,mtz_ref_file=mtz_ref_file) File "~opt/phenix-1.9-1692/phenix/phenix/wizards/AutoBuild.py", line 7696, in run_standard_build_in_parallel r.run(out=sys.stdout) File "~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line 294, in run self.start_run(run_file,last=is_last) File "~opt/phenix-1.9-1692/phenix/phenix/autosol/run_group_of_wizards.py", line 604, in start_run cmd+" "+self.add_double_quote(run_file,escape_space=False)).raise_if_errors() File "~opt/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 37, in raise_if_errors raise Error(msg) RuntimeError: child process stderr output: command: 'qsub background=False nproc=20 "~phenixWorkingDir/1yya/part1/8tim/AutoBuild_run_5_/TEMP0/RUN_FILE_1"' /bin/sh: qsub: command not found XXXXXXXXXXXXXX Please let me know if I can share eff and log files of the run. Please advice, Kaushik -- People living deeply have no fear of death - Anais Nin Caution: I am still the dumbest person I have ever known :-)

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FEM map calculation without model?
by Oliver Clarke 28 Apr '15

28 Apr '15

Hi all, Is there any way to apply the local map sharpening and histogram equalization procedures described as part of the FEM map generation procedure (described in “FEM: feature-enhanced map”, Afonine et al,mActa D71 2015) to an MTZ containing amplitudes and phases only, without a model (e.g. as generated by phenix.map_to_structure_factors)? I would like to see if these different approaches to map modification are useful for improving maps derived from cryoEM. I guess there is no way to do the random map perturbation part of the FEM procedure without a model, but the sharpening and histogram equalization seem like they might be applicable? Best, Oliver.

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Scientist position -- Protein Crystallization at AbbVie, North Chicago
by WEi WEi 28 Apr '15

28 Apr '15

*Scientist II, Structural Biology - Crystallization-1500000257* AbbVie (NYSE:ABBV) is a global, research-based biopharmaceutical company formed in 2013 following separation from Abbott Laboratories. The company's mission is to use its expertise, dedicated people and unique approach to innovation to develop and market advanced therapies that address some of the world's most complex and serious diseases. AbbVie employs approximately 26,000 people worldwide and markets medicines in more than 170 countries. The Structural Biology organization has an exciting opportunity for a Scientist I or Scientist II (depending on experience) to join the Crystallization group to support AbbVie's new collaboration with Calico. The Scientist will conduct biological macromolecule crystallization experiments in support of structure based drug design. The selected candidate must be knowledgeable in protein handling and characterization techniques and possess excellent communication skills. The Scientist will be expected to consistently work on multiple projects in parallel and be able to adjust to rapidly changing priorities. In addition, this individual will be highly self-motivated, able to work independently in their area of expertise and work collaboratively with cross-functional teams. For detail information, please visit the link below and apply online using the Job ID: *1500000257. * https://abbvie.taleo.net/careersection/2/jobsearch.ftl?lang=en Thanks, Wei

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Global real-space refinement
by oleg＠quantumbioinc.com 27 Apr '15

27 Apr '15

I have a question. What does trigger Global real-space refinement ? I never seen it before except one structure I am currently working on. Also I do not see any options that switch on/off "Global real-space refinement " Please advise Oleg

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Automatic linking of glycans doesn't work when hydrogens are added by ReadySet
by Tristan Croll 27 Apr '15

27 Apr '15

Hi, I'm currently using the dev 2000 version of Phenix, and noticed an issue with the automatic linking of N-linked (and presumably O-linked) glycans. If you feed a glycosylated structure sans hydrogens to Phenix and allow ReadySet to add hydrogens prior to refinement, it adds hydrogens as if the glycans are unlinked. Then, the automatic linking script rejects them due to valence issues. Cheers, Tristan

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idealizing structure
by PC 27 Apr '15

27 Apr '15

Is there a way to "idealize" a structure in Phenix? I mean, ideal omega, all residues within allowed regions of Ramachandran maps, no clashes..etc. I know it won't fit the map well but I would like to see what it looks like. Thank you. ____________________________________________________________ FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your desktop! Check it out at http://www.inbox.com/marineaquarium

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Re: [phenixbb] citation
by Sneha Rangarajan 27 Apr '15

27 Apr '15

Hello All, I have a non-Phenix problem- finding shape complementarity! I tried running the script for sc (ccp4) but it doesn't run to completion to give me the sc number. It stops saying "imaginary contain". What does that mean? However there is no error as such. I gave it the pdb that I got after my phenix refinement. Is there something I should be doing first to the pdb after refinement before running sc on it? Here is the script and I am also attaching the pdb. sc XYZIN F7-2_refine_113.pdb <<eof-sc MOLECULE 1 CHAIN A CHAIN B MOLECULE 2 CHAIN C eof-sc Thanks in advance!! Sneha From: Randy Read [mailto:[email protected]] Sent: Tuesday, April 21, 2015 3:42 AM To: Sneha Rangarajan Subject: Re: [phenixbb] citation Dear Sneha, Here's a link to the publication (which is open access): http://scripts.iucr.org/cgi-bin/paper?ba5210. Best wishes, Randy Read On 20 Apr 2015, at 19:02, Sneha Rangarajan <rsneha(a)umd.edu<mailto:[email protected]>> wrote: Hello, What is the correct way to cite Phenix MRage? Thanks, Sneha _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]> ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk<mailto:[email protected]> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk<http://www-structmed.cimr.cam.ac.uk>

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rigid_body refinement
by Irina PROKHOROVA 24 Apr '15

24 Apr '15

Hello, how can i select two chains to be refined as one rigid body? I tried refinement.refine.sites { rigid_body = chain A and chain B } but it did not work. Irina

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on Cutting out density by Phenix
by Smith Liu 23 Apr '15

23 Apr '15

Dear All, I have tried to cut out the density by the Phenix graphical interface with the cutout type as model, but I find in the cut out map, there is more density arond the residues than in the input mtz map, here I mean, take a Lys residue as an example, in the input map, from Calpha there is about 1/2 of the sidechain was surrounded by the density, but in the cutting out map, there is about 2/3 of the sidechain was surrounded by the density. Will you please tell me if I want to get the cutting out density in the model cutout type, how can I have the cutting out density looks exactly or very close to the input density in the input mtz? Smith

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Generating cif file for DNA basepairing in PHENIX
by 李翔 22 Apr '15

22 Apr '15

Hi everyone, I am trying to build some DNA duplex models with different pitches by 3DNA. After changing the pitches from the original duplex model, I refined the duplex in PHENIX with geometry minimization. However, the basepairing get completely distorted. Is there a quick way to generate the cif file for basepairing in PHENIX or are there any other better ways to keep the basepairing restraint during the model refinement? Thank you very much for your kind help! Sincerely, Xiang -- Li Xiang Department of chemistry, University of Michigan Email：lixiang1642(a)gmail.com

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on the convergence of the Phenix refine
by Smith Liu 22 Apr '15

22 Apr '15

Dear All, Suppose I have a refine of 10 cycles, it get stablized from cycle 7. But sometimes I noticed that from the end of the cycle 10 to the end of the whole refinement, the stablization from 7 to cycle 10 can be destroyed a little, which makes me concern whether the final refinement can be regarded as convergent or not. Will you please explain why the stablization from 7 to cycle 10 can be destroyed a little from the end of cycle 10 to the end of the whole refinement? More critically, in the other situation, suppose I have a refine of 10 cycles, it get relatively stablized from cycle 5, from the end of cycle 5 to the end of cycle 10 the Rfree increase very slightly each cycle of the refine, which makes at the end of cycle 10 the Rfree is slightly higher than the Rfree at the start of the whole refinement. But from the end of cylce 10 to the end of the whole refinement, there is a slight decrease of Rfree, which makes the Rfree at the end of the whole refinement slightly lower than Rfree at the start of the whole refinement. It seems to increase the cycles of the refinement would not help further. Will you please explain the above phenomenon and to see whether the refine result can be acceptable, or do you have any suggestions for improvement? Smith

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Off-topic: Hydrogen images
by mohamed noor 21 Apr '15

21 Apr '15

Dear all I will be presenting about protein crystallography to a group of PhD-level physicists and need some images from the community. Would anyone have high-quality images of density maps that show hydrogen atoms at 1. high and ultra-high X-ray resolution (say, about 1.2 A to about 0.5 A) 2. low or medium X-ray resolution (where H atoms are not visible) compared with neutron data (with H). Ideally these images should be from the same protein so that I can show the power of complementary beam source for the diffraction. A side question - what is the community's preference to get deuterated samples? Is it crystal soaking or growing E. coli in deuterium? All contributions will be credited. Thanks.

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citation
by Sneha Rangarajan 21 Apr '15

21 Apr '15

Hello, What is the correct way to cite Phenix MRage? Thanks, Sneha

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Standard settings for map generation in phenix.refine
by Tristan Croll 21 Apr '15

21 Apr '15

Hi all, In the phenix.refine GUI, the default options for the maps auto-generated in Coot include the R-free set in the map coefficients. Is this the best choice? It's fairly natural for the user to immediately inspect/correct their structure using the helpfully-provided Coot window - which, as per a recent discussion thread on this list, can easily lead to over-fitting. I suspect I've been looking at such a case over the last week or so - a mid-3A structure refined in Phenix with an amazingly low Rfree (0.234) and Rfree-Rwork (~0.016), despite clear (albeit non-disastrous) errors in a number of loops, and moderate-poor statistics in structural quality metrics. Tellingly, the Rfree goes up quite substantially upon re-refinement after correcting these issues. If maps generated with the Rfree set included should only ever be used for final display, wouldn't it be better to have them excluded by default? Best regards, Tristan Tristan Croll Lecturer Faculty of Health School of Biomedical Sciences Institute of Health and Biomedical Engineering Queensland University of Technology 60 Musk Ave Kelvin Grove QLD 4059 Australia +61 7 3138 6443 This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.

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on importing CIF structure factors and cutting out density
by Smith Liu 21 Apr '15

21 Apr '15

Dear All, By importing CIF structure factors of the Phenix graphical interface, I converted a CIF file to a mtz file. But when I tried to cutting out the density by Phenix with the converted mtz file, it request the map labels, which the converted mtz file seems does not have. Will you please let me know how to have the issue settles? Smith

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phenix refinement of cryoEM data
by Ali Malay 17 Apr '15

17 Apr '15

Dear all, I am a relative newcomer to Phenix. I have a large multimeric protein structure docked into an electron density map, and I would like to further refine it by rigid-body refinement using Phenix. Is this a realistic strategy? I have made some attempts, first by converting the .mrc map file to .mtz as outlined here: https://www.phenix-online.org/documentation/reference/map_to_structure_fact… <https://www.phenix-online.org/documentation/reference/map_to_structure_fact…> Then I tried to refine using rigid body refinement in Phenix. However, the program quits but doesn’t really tell me why. Here’s the last part of the log file: Number of unique models: 24 Time building chain proxies: 36.85, per 1000 atoms: 0.26 Number of scatterers: 142296 At special positions: 0 Unit cell: (342, 342, 342, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 264 16.00 O 27720 8.00 N 25872 7.00 C 88440 6.00 sf(0) = scattering factor at diffraction angle 0. Writing MTZ file: /Users/xxx/Documents/Phenix/TEST/Refine_1/Test_refine_data.mtz Sorry Can anyone give me any ideas as to what went wrong? Also, is there a better way to do this? Thanks very much in advance!! A.M.

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find difference peaks
by Alejandro Virrueta 16 Apr '15

16 Apr '15

Hello, I'm working on a small project, and need some feedback. I am trying to rebuild methionine side-chains by looking at the difference peaks for a given Fo-Fc map. I envision a process as follows: 1. Delete the MET side-chain of a PDB file 2. Refine structure to get Fo-Fc map 3. Get a list of the peak positions relative to the coordinates of the PDB file I used 4. Filter list by keeping peaks near the MET C alpha/beta PDB coordinate. 5. Try to rebuild side-chain after anchoring the sulfur atom (assuming sulfur is located at the highest peak and within some distance to C beta) What functions should I use to achieve step 3? I am also trying to implement this process within the ringer program (phenix/cctbx_project/mmtbx/command_line/ringer.py). If anyone is familiar with this, what commands would work best within this ringer program? i.e. what functions can operate on difference_map (which is sampled by a point using tricubic_interpolation under 'def sample_angle')? I hope this makes some sense to someone. Thanks! Alex

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reflections file editor
by Almudena Ponce Salvatierra 14 Apr '15

14 Apr '15

Dear all, I would like to merge two datasets containing anomalous signal. If have done so earlier for native data within phenix in the reflections editor by selecting the arrays corresponding to FP and SIGFP and then running the program. However when I try to do so for the anomalous datasets it writes FP SIGFP and FP2 SIGFP2 instead or merging them, so it does with the anomalous signal... so I guess I have basically only one file containing two datasets but not a merged dataset. How can I solve it? Would it be possible, on the other hand, to merge a dataset with anomalous signal with a native one? The intention behind is to extend the resolution to the one of the native data. Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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sugar puckering refinement with phenix refine
by Almudena Ponce Salvatierra 14 Apr '15

14 Apr '15

Dear all, does anyone know how phenix.refine deals with the sugar puckering of an RNA or a DNA strand? Does it refine it? Or does it leave it as it was built? Thank you very much in advance. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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Link NGA and THR
by Cory Brooks 13 Apr '15

13 Apr '15

Hello! I am refining a structure with O-link glycosylation (GalNAc linked to Thr). Phenix seems to remove the link during refinement. Can anyone suggest a solution that will maintain the bond during refinement? Regards, Cory Cory Brooks,Ph.D.

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elbow-readyset
by Tarek DawoD 13 Apr '15

13 Apr '15

Dear All if i have pdb file for CdCl2, how could i generate cif file (to use later in phenix.refine) from that using readyset or elbow or any other tool.i could not find 3 letter could for CdCl2. COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.1 HETATM 1 CD LIG 1 0.994 8.428 20.546 1.00 0.00 Cd HETATM 2 CL1 LIG 1 -0.441 6.507 20.373 1.00 0.00 Cl HETATM 3 CL2 LIG 1 3.190 7.731 21.231 1.00 0.00 Cl END Thank you for Help.regardsTK_DawoD

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Submit your abstract for the ACA Annual meeting in Philadelphia July 25-29, 2015
by Terwilliger, Thomas Charles 13 Apr '15

13 Apr '15

Hi Phenix users! You are invited to the ACA meeting in Philadelphia! Abstracts are still being accepted (see the invitation below). All the best, Tom T Tom Terwilliger Vice President, ACA Abstracts still being accepted ACA 2015 Meeting - July 25-29 Philadelphia, PA Is this email not displaying correctly? View it in your browser<http://us2.campaign-archive2.com/?u=3e43dd9d1724b97d2bc286881&id=0f524b9d2c…>. [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/2a8238a9-d30…] [http://www.amercrystalassn.org/2015-mtg-homepage]<http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2b…> ABSTRACT SUBMISSION DEADLINE IS EXTENDED ACA Annual Meeting • Philadelphia, PA • July 25 - 29, 2015 Submit abstract now to be considered for an oral presentation. Once all the lectures are scheduled, abstracts will continue to be accepted for poster presentations. [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/21952137-733…] Exhibit Show<http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2b…> First-time exhibitors receive 25% discount Discount rates for Not-for profits Corporate Members receive an additional discount Coffee breaks & poster sessions held in the exhibit hall to offer multiple opportunities to reach your target audience Your website linked on the meeting page Free listing in ACA RefleXions and Program & Show Guides Special sponsorships for Exhibitors only [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/d9f63f39-b8b…] Call for Papers:<http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2b…> 40% of talks selected from contributed abstracts No abstract submission fee Lower registration fees for members Sessions for students & young scientists on career directions, reviewer practices & more Full scientific program:www.AmerCrystalAssn.org<http://amercrystalassn.us2.list-manage1.com/track/click?u=3e43dd9d1724b97d2…> [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/961e8c70-86c…] Registration<http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2b…>: Join or pay membership dues and save on Registration fees Corporate Members receive advertising and exhibiting discounts Early bird rates until May 31 Online registration now open<http://amercrystalassn.us2.list-manage2.com/track/click?u=3e43dd9d1724b97d2…> follow on Twitter<Twitter%20Account%20not%20yet%20Authorized> | friend on Facebook | forward to a friend<http://us2.forward-to-friend.com/forward?u=3e43dd9d1724b97d2bc286881&id=0f5…> Copyright © 2014, AmericanCrystallographicAssn. All rights reserved. Our mailing address is: aca(a)hwi.buffalo.edu<mailto:[email protected]> ACA, PO Box 96, Buffalo, NY 14205 [Email Marketing Powered by MailChimp]<http://www.mailchimp.com/monkey-rewards/?utm_source=freemium_newsletter&utm…> unsubscribe from this list<http://amercrystalassn.us2.list-manage.com/unsubscribe?u=3e43dd9d1724b97d2b…> | update subscription preferences<http://amercrystalassn.us2.list-manage.com/profile?u=3e43dd9d1724b97d2bc286…>

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pdbtools: how to set the occupancy for an atom selection?
by Alejandro Virrueta 13 Apr '15

13 Apr '15

Hello, I was wondering if someone could show me a way to set the occupancy of a specific set of atoms to 0 using phenix.pdbtools. I noticed here <http://www.phenix-online.org/download/documentation/cci_apps/pdbtools.html#…> that there is no option under modify => occupancies to do an 'atom_selection'. Any help would be appreciated. Cheers, Alex

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Deposition question
by mohamed noor 13 Apr '15

13 Apr '15

Dear all I solved my structure using SAD from heme to 2 A and then did molecular replacement with a dataset diffracting to 1.2 A. Do I deposit only the mtz and pdb file from the last refinement run and report the corresponding statistics in 'Table 1'? Should I specify the experimental f' and f'' values? Thanks.

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expermiental sigma or SIGFP of the mtz file
by Smith Lee 13 Apr '15

13 Apr '15

Dear All, Will you please let me know what is the expermiental sigma or SIGFP of the mtz file? If a mtz file lacks the expermiental sigma or SIGFP, what does it mean? I am looking forward to getting your reply. Smith

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Reference model restraints in real space refinement?
by Oliver Clarke 12 Apr '15

12 Apr '15

Hi all, Is it possible to use reference model restraints at the moment during real space refinement (in phenix.real_space_refine)? I can’t see it in the documentation. On a related note, would it be possible at some point to allow users to set d_max in the phenix.map_to_structure_factors utility? At the moment it seems like the user can set d_min but not d_max - sometimes it is convenient to restrict the low res to 20 or 50Å, rather than the whole box size of an EM-map, which is the default. Best, Oliver.

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Phenix command to align the PDB sequence and input sequence
by Smith Liu 11 Apr '15

11 Apr '15

Dear All, Will you please tell me the Phenix command to align the PDB sequence and input sequence? I am looking forward to getting your reply. Smith

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Error refining with ramachandran restraints
by Oliver Clarke 10 Apr '15

10 Apr '15

Hi all, When I attempt to run a refinement using phenix.refine from the command line, using the parameter “ramachandran_restraints=true”, in the latest nightly build of phenix (dev-2006), I get the following error: ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. Traceback (most recent call last): File "/Applications/phenix-dev-2006/build/../modules/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Applications/phenix-dev-2006/modules/phenix/phenix/refinement/command_line.py", line 96, in run master_params=customized_master_params) File "/Applications/phenix-dev-2006/modules/phenix/phenix/refinement/driver.py", line 272, in __init__ secondary_structure_manager=self.sec_str, AttributeError: refine instance has no attribute 'sec_str' This happens for two different structures, so I don’t think it is a structure-specific thing, and I don’t recall this happening in older builds of phenix. The refinement runs fine if I don’t specify ramachandran restraints. Is there something obvious I am doing wrong? Best, Oliver.

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Autobuild error
by Lau Sze Yi (SIgN) 08 Apr '15

08 Apr '15

Hi, I did an Autobuild run. The Status panel indicated that the run is finished. In the Model building panel the status of run# 5 still says running (See attached screenshot). Is this normal? And when I click on run #4 to Open in Coot, I get an error message indicating that the directory could not be found (see attachment). What is wrong and how can I fix this? I am using version phenix-1.9-1692 on Mac. Regards, Sze Yi Research Fellow Singapore Immunology Network (SigN) 8A Biomedical Grove, #03-06 Immunos, Singapore 138648 DID: +65 6407 0640 Fax: +65 6407 0640

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on reciprocal space refine of the electronic microscopy map by Phenix
by Smith Liu 08 Apr '15

08 Apr '15

Dear All, Recently there are cryo-electronic microscopy papers which refine the reciprocal space of the electronic mcroscopy map by phenix refine. For the electronic mcroscopy map, what does it mean for the reciprocal space? How to get the reciprocal space map from the electronic mcroscopy map? In order to realize this kind of refine in phenx, we only process the xyz coordinates strategy refine in the graphical interface, right? I am looking forward to getting your reply. Smith

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FINAL REMINDER: Neutrons in Structural Biology
by Meilleur, Flora 06 Apr '15

06 Apr '15

6th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 1 - June 5, 2015 Application deadline: April 10, 2015 Detailed information can be found on the workshop web page: https://public.ornl.gov/neutrons/conf/gcnb2015. 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

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