- phenixbb - phenix-online.org

metal-ligand distances, and Optimize X-ray/stereochemistry weights
by Emilia C. Arturo (Emily) 21 May '15

21 May '15

I'm refining a model at 2.9 A, where four chains are in the ASU, and each active site has an iron with a few ligands; the configuration of this active site is the topic here. Currently the iron-ligand distances are not ideal (according to CheckMyMetal and the ideal distances generated by phenix.metal_coordination), but they are within a range observed previously for structures of truncated versions of this enzyme; furthermore, the more the metal-ligand distances change towards ideal distances, the more positive and negative density I observe in the Fo-Fc, so it appears that this deviation from the 'ideal' is supported by the data. However, when I use the 'Optimize X-ray/stereochemistry weights' option during refinement, the metal-ligand distances change (the metal appears to do most of the moving), getting closer to ideal, and this generates more positive and negative density in the Fo-Fc map). However, clearly it's nice that optimizing the X-ray/stereochemistry weights reduces R-free (and keeps the R-f/R-work ratio fine as well). So what is the most appropriate approach here, in order to keep the metal-ligand distances that best support the data, but still reap the benefits of the optimized stereochemistry weights? Some details of the structure and refinement are these: The iron in each of the four chains in the ASU is coordinated with atoms from two histidines, a glutamate, and a water (so four ligands per Fe) and there remains un-modeled density in the iterative build comp OMIT map used for modeling (because resolution is 2.9A and adding more water (which is my best guess, given what truncated structures at higher resolution show coordinating the Fe) does nothing to the Rf). I am working with an .edits file generated by phenix.metal_coordination. After some experimentation, I've left the sigma values (for Fe-O and Fe-N) at default values, and added a restraint for Fe-O (water), using an ideal distance of 2.3 and a sigma value of 0.1. Emily.

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Your abstract can still be considered for an oral presentation at the American Crystallographic Assn Annual meeting
by Terwilliger, Thomas Charles 21 May '15

21 May '15

Hi Phenix users, A message from the American Crystallographic Association! YES! We are still accepting abstracts. No late fee. ACA Annual Meeting • Philadelphia, PA • July 25 - 29, 2015 Submit now to be considered for an oral presentation. Once all the lectures are scheduled, abstracts will continue to be accepted for poster presentations. see: http://www.AmerCrystalAssn.org All the best, Tom T Vice-President, ACA

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on B-factor refine of the phenix.real_space_refine
by Smith Liu 20 May '15

20 May '15

Dear All, I have a EM map (.mrc), with fitting and based on a crystal structure I got the fitted PDB file. I convert the mrc map to the CCP4 map， and I run phenix.real_space_refine model.pdb map.mtz run=adp, with phenix-dev-2034, in order to get my own b-factors for my fitted PDB based on my EM map. However after the above phenix.real_space_refine, I checked the refined PDB, and I find phenix.real_space_refine neither change the coordinates, nor change the b-factors for each atom. Thus will you please introduce to me how can I get my own b-factors for my fitted PDB in order to deposit my map and fitte pdb to the EM database? Smith

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Map quality
by mohamed noor 19 May '15

19 May '15

Dear all Is there a single (or a few) metrics that can be used to quantitatively assess map quality instead of looking at each one in Coot? For example, I want to compare the effect of having low completeness in the low resolution shells. Thanks.

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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 12 May '15

12 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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