Search results for "look through"

Re: [phenixbb] XDS data

by Tim Gruene

Dear Nat, I won't need to send the header, the first line looks as you expect. FRIEDEL'S_LAW=TRUE in the XDS_ASCII.HKL does not mean that the Friedel pairs are merged (it would, though in XSCALE output in combination with MERGE=TRUE). The former keyword affects the scaling, and both Wolfgang Kabsch and George Sheldrick are of the opinion the scaling gives better results by using twice the number of data without hampering with the data quality by ignoring the anomalous differences. XDS does not have the keyword 'merge', only xscale does, but there is not reason to scale the data twice, as XDS output data are already scaled. I will see how far I get with xscale output, but scientifically it would be beneficial for phenix to allow said XDS format (I agree that shelx hkl-format is not a joy for GUIs). We are using the latest release, version 1.8.4. Cheers, Tim On 01/14/2014 04:53 PM, Nathaniel Echols wrote: > On Tue, Jan 14, 2014 at 4:42 AM, Tim Gruene <tg(a)shelx.uni-ac.gwdg.de> wrote: > >> I would like to run Phaser-EP through the phenix GUI. When I first >> uploaded the XDS_ASCII.HKL file, there was an error message about "No >> valid observed reflections found in this file". > > > Can you send me the first three lines of the file? My guess is that it > looks like this: > > !FORMAT=XDS_ASCII MERGE=FALSE FRIEDEL'S_LAW=TRUE > > which would be interpreted by our XDS reader as being non-anomalous, even > though since it's unmerged there is probably nothing stopping us from using > the anomalous data anyway. (I need to double-check this, because I don't > understand why it would claim "FRIEDEL'S_LAW=TRUE" if I+ and I- are > actually kept separate.) If you instead produce a file that starts like > this: > > !FORMAT=XDS_ASCII MERGE=TRUE FRIEDEL'S_LAW=FALSE > > then it will be accepted by the Phaser-EP GUI. > > Subsequently I >> uploaded an unmerged hklf4 file. The GUI tells me I need to let phenix >> know about it being hklf4 by appending '=hklf4'. However, when I do >> so, there is an error message the file did not exist and the Data file >> line goes red. Where should I correctly append '=hklf4'? >> > > This may simply be a bug. Which version are you using? I had attempted to > make the GUI handle SHELX files more sensibly (to the extent that's even > possible), but I can't remember how successful I was, and it may have been > after version 1.8.4 was released. In general, SHELX format is the least > compatible of the supported inputs; it's just missing too much information. > > -Nat > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A

12 years

Re: [phenixbb] high average b-factor vs. Wilson B - EXPLANATION

by Pavel Afonine

Hi Geoffrey, thanks for sending me the data and model - this helped me to find out what happens in your and other similar repeatedly reported cases. Have a quick look at the total model structure factor formula that is used in all phenix.refine, phenix.model_vs_data, phenix.maps and many other similar tools: see page 6 here: http://www.phenix-online.org/presentations/latest/pavel_refinement_general.… and glance through the page 29, PHENIX Newsletter: http://www.phenix-online.org/newsletter/CCN_2010_07.pdf As you see there is overall anisotropic scale matrix Ucryst (see /Acta Cryst./ (2005). D*61*, 850-855 and references therein for deeper level of details). In refinement, the trace of this matrix is subtracted from it and added to individual ADPs and Bsol, making Fmodel invariant under this manipulation. Most of the time, this is a small value, but sometimes it is relatively large. Now, let's see what happens in your particular case. The Wilson B-factor is 27. If we reset all B-factors to 27 and repeat the refinement until convergence using two scenarios: 1) we add the trace of Ucryst to individual ADPs, 2) we do not add the trace of Ucryst to individual ADPs, we will get the following: 1) R-work = 0.1728, R-free = 0.2177 Bcryst (Ucryst reported as B) = (-10.42,-11.48,21.90,-0.00,0.00,0.00); trace/3= 0.00 ksol= 0.33 Bsol= 54.75 Average ADP = 43.56 2) R-work = 0.1744, R-free = 0.2171 Bcryst (Ucryst reported as B) = (4.42,3.35,36.58,0.00,0.00,0.00); trace/3= 14.78 ksol= 0.32 Bsol= 40.00 Average ADP = 29.03 Clearly, in case "2)" you get almost exact match of Wilson B and Average ADP (27 and 29), while in case "1)" the B-factors are higher. Note, the R-factors in both cases are "identical" (negligibly different given the resolution and the R-factor value). So I guess everything is more or less consistent and clear. It depends where and how you keep different contributions to the total ADP, and which values you use to compute mean ADP. Answering your very original question "Should I be concerned about this?": the answer is no. But I had a quick look at your maps: and this is what I would spend some more time: you have a lot of positive and negative peaks, some of them are very strong: larger than 6sigma! I guess you are missing some ions, and alternative conformations may need some more attention. This is normal, it just needs some care and time to be spent before your structure is ready to go (to PDB). Pavel. PS> I'm sending you the results of these two runs off list. On 8/3/10 10:20 PM, Geoffrey Feld wrote: > Dear PhenixBBers, > > I'm working on a 1.45 A structure I solved using MR (phaser) and I'm > pretty close to finishing, just plopping in waters and fixing > rotamers. Rw = 19.8 Rfree= 22.8. I am a little concerned because my > Wilson B is 27.00 while my average B for macromolecule is more like > 43, and for solvent is 48. I have enough data to use anisotropic ADP > refinement, which was a big help in bringing down the Rfree, but the > average B hasn't really moved much. Should I be concerned about this? > Should I try adjusting the wxu, or some other parameter? > > Thanks!

15 years, 6 months

Re: [phenixbb] Out of Memory Errors

by Randy Read

Hi, The current defaults in Phaser are not kind to memory consumption for large cases. As it happens, we're working on changing those defaults sensibly so that the memory usage will depend much less on the size of the problem, and hopefully also so it recovers more gracefully when an attempt to allocate memory fails. In the meantime, you'll have to switch to Phaser-MR to avoid all memory issues, because AutoMR lacks some of the fine control. The main thing you can do is to reduce the resolution in proportion to the mean radius of the assembly you're looking for. (In practice this means that the resolution should be proportional to the cube root of the molecular weight -- if you would use 2.5A data for a 30kDa model, then use 5A data for a 240kDa model. On that basis, even 4A is generous for your 12x48kDa search model.) This will get you through everything but the final refinement step, where by default Phaser carries out rigid-body refinement against all data. In the Phaser-MR GUI, there's a box labelled "High resolution for refinement", and you'll have to set that at something less than the full resolution. Apart from resolution, you can look at our FAQ on memory consumption, which you can find at http://www.phaser.cimr.cam.ac.uk/index.php/FAQ, and that discusses some of the other expert parameters you could set to reduce memory needs. However, in your case it's not clear to me why you would want to run molecular replacement with a model containing four trimers. Is the structure really a dodecamer? If not, then I wouldn't want to assume that the relationship among trimers is conserved from one crystal to another. Best wishes, Randy Read On 20 Apr 2011, at 21:08, Heather Condurso wrote: > Hello all, > > I am currently running the Phenix GUI version 1.7-650 on an iMac with an 3.2Ghz Intel Core i3 processor, 8GB of memory operating under OS 10.6. During many of my runs (mostly AutoMR runs but sometimes refine) I get out of memory errors. I have my system booted in 64 bit mode and I watch the activity monitor and find that phenix doesn't use much more than 2GB of memory. My search model is very large. My unit cell contains 4 trimers (each monomer is 48kDa). I hadn't encountered this issue until I began to increase my search model from one trimer to four. Do you have any suggestions as to how I could avoid this error without minimizing my search model? Often my AutoMR runs get the out of memory error at the start of refinement, but just now the memory was exhausted during the fast rotation function. During this run I used all default parameters with a max res of 4.0 and RMSD of 1.0. > > Any advice you can give would be greatly appreciated! > Heather > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb ------ 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 Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

14 years, 9 months

Re: [phenixbb] Discrepancy between Phenix GUI and command line for MR

by Xavier Brazzolotto

Hi Randy, Indeed I’m running Phenix on a brand new M2 Mac. I will benchmark the two processes (GUI vs command line) and post them here. > Le 4 juil. 2023 à 12:32, Randy John Read <rjr27(a)cam.ac.uk> a écrit : > > Hi Xavier, > > We haven’t noticed that, or at least any effect is small enough not to stand out. There shouldn’t be a lot of overhead in communicating with the GUI (i.e. updating the terse log output and the graphs) but if there is we should look into it and see if we can do something about it. > > Could you tell me how much longer (say, in percentage terms) a job takes when you run it through the GUI compared to running the same job outside the GUI on the same computer? Also, it’s possible the architecture matters so could you say which type of computer and operating system you’re using? If it’s a Mac, is it one with an Intel processor or an ARM (M1 or M2) processor? (By the way, we finally managed to track down and fix an issue that cause Phaser to run really slowly on an M1 or M2 Mac when using the version compiled for Intel, once I got my hands on a new Mac.) > > Best wishes, > > Randy > >> On 4 Jul 2023, at 10:44, Xavier Brazzolotto <xbrazzolotto(a)gmail.com> wrote: >> >> Dear Phenix users >> >> I’ve noticed that molecular replacement was clearly slower while running from the GUI compared to using the command line (phenix.phaser). >> >> Did you also observe such behavior? >> >> Best >> Xavier >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building > Hills Road E-mail: rjr27(a)cam.ac.uk > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk >

2 years, 7 months

Re: [phenixbb] command line molprobity tools

by Engin Özkan

Thanks Pavel. This does half the job by reporting the overall values, but does not list detail. For example, it tells you the Ramachandran outlier percentage, but does not list the outlier residues. Or the bond and angle outliers. I would like to see those output as well. These are all done beautifully in the GUI, but apparently not output as human-readable text files. I looked at full parameter list, but could not see a longer output switch. Engin On 5/1/13 12:19 PM, Pavel Afonine wrote: > Hi Engin, > > try: > > phenix.pdbtools model_stat=true model.pdb > > If this doesn't do what you want then please let me know. > > Pavel > > On 5/1/13 12:15 PM, Engin Özkan wrote: >> Hi everybody, >> >> I want to create a comprehensive, human-readable log file by running >> validation using molprobity tools within phenix command-line. I do >> not have structure factors/maps. Apparently, the GUI runs validation >> through phenix.model_vs_data (according to the .eff file), but in >> command-line, I cannot get phenix.model_vs_data to run without an >> mtz/hkl. I guess I could provide it a fake data file, and then set >> the comprehensive flag to "True"? BTW, the log file produced by the >> GUI is not comprehensive at all. >> >> I could not find a related mmtbx or cctbx function either. Another >> mentioned tool, phenix.validate, does not even exist in my >> installation (dev 1361). >> >> Thanks, >> Engin >> > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 w ph: (650)-498-7111 cell: (650)-862-8563

12 years, 9 months

[phenixbb] helix/sheet outliers

by Casper Larsen

Hi.. I am doing real space refinement on a protein model build from a cryo-em map. I run the refinement with Amber gradients turned on and with secondary structure restraints (otherwise, more or less default settings). I have some issues with helix and sheet outliers. Every time I run the refinement (after making sure that the bond distance in the helices are within the 3.5 Å) I get a lot of bad annotation remarks, but with outliers just above 3.5 Å (see .log below): ... removed outlier: 3.576A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 3.681A pdb=" N PHE A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.737A pdb=" N MET A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) ... Is this something that I just need to fix in several rounds of refinement or is there an explanation? Amber gradients maybe? In addition, I have some bad sheet annotations such as: ... removed outlier: 6.987A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) ... When I look at the model, the residues are definitely a part of the sheet - the long distance between the N-O atoms is due to the O being "flipped" (hope it makes sense). Is this because of wrong annotation? Best Casper

5 years, 9 months

Re: [phenixbb] Missing plotting libraries

by William G. Scott

Maybe you need this: http://packages.ubuntu.com/jaunty/libs/liblapack3gf On May 4, 2009, at 10:14 AM, Leigh Allen wrote: > ERROR: > > Reading package lists... Done > Building dependency tree > Reading state information... Done > E: Couldn't find package lapack3 > > Thanks for your help. I've tried installing lapack and/or lapack3 > through > apt-get and synaptic... and I can't find it. I'll continue looking > and > potentially ask the Ubuntu people since this is not a Phenix problem. > > Thanks again, > Leigh > > On Mon, May 4, 2009 at 1:00 PM, Nathaniel Echols <NEchols(a)lbl.gov> > wrote: > >> On May 4, 2009, at 8:56 AM, Leigh Allen wrote: >>> How do I fix this? >>> You appear to be missing one or more libraries required by the >>> plotting module; plots will be disabled for now. The original >>> error is shown below. >> >> As Ralf said, the quick solution is to install lapack - it's usually >> there already, but some systems don't include it by default. On >> Ubuntu, "apt-get install lapack3" will take care of it. I will see >> if >> I can add it to the installer - this will probably not happen until >> next week, though. For now, I've fixed the code so it will fail more >> gracefully if plotting is disabled - that will be in 1.4-56 (tomorrow >> morning). >> >> thanks, >> Nat >> >> ------------------- >> Nathaniel Echols >> Lawrence Berkeley Lab >> 510-486-5136 >> NEchols(a)lbl.gov >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb

16 years, 9 months

Re: [phenixbb] phaser MR

by sbiswas2＠ncsu.edu

Hi Francis, Thanks for your response. The matthews coefficient suggests two molecules in the AU. Phaser also finds two molecules. I ran the dataset through phenix xtriage it did not indicate twinning though. The molecule also exists in nature as a monomer. Shya > Twinning? What's your matthews coefficient say? Do you know if your > structure is a multimer (biochemistry, etc)? Does it agree with the > matthews coefficient? > > If the unit cell is not big enough to hold all of the contents,then > this is an indicator for twinning . > > FR > > On Jul 23, 2009, at 3:09 PM, sbiswas2(a)ncsu.edu wrote: > >> Hi all, >> >> I was trying to solve a structure by molecular replacement. I scaled >> the >> data in P4222 space group (resolution 2.7A) with two molecules in the >> assymmetric unit (molecule A and B) I ran phaser with my model and >> got a >> Zscore of 5.1. When I look at the map that I got from phaser I could >> easily see good electron density for both molecules, However upon >> inspection of the electron density map there were considerable >> interaction >> or clashes with molecule B and a symmetry atom. Molecule A had no >> clashes >> however with the symmetry atoms. I was wondering if anyone knows how >> to >> resolve this. Could it be a problem of space group. The statistics >> are >> good for space group P4222 and the I/sigI was good till 2.7A. >> Any advice is appreciated, >> Shya >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb > > --------------------------------------------- > Francis Reyes M.Sc. > 215 UCB > University of Colorado at Boulder > > gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D > > 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

16 years, 6 months

[phenixbb] Application deadline is this week: CCP4/APS crystallographic school, June 21 - 29, 2016

by Sanishvili, Ruslan

Dear Colleagues, Deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered. If you have a crystallographic problem you cannot resolve independently, this school is for you. From our past experience, the majority of participants bring with them the crystallographic problems and almost all these problems are resolved at the school. Some of the publications, acknowledging the contribution of the school, are listed at http://www.ccp4.ac.uk/schools/APS-school/publications.php This school will cover popular packages such as CCP4, PHENIX, SHELX and much, much more: http://www.ccp4.ac.uk/schools/APS-2016/program.php Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts. Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue. These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found at: http://www.ccp4.ac.uk/schools/APS-2016/index.php We are looking forward to meeting you in Argonne this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. 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 ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Wednesday, March 23, 2016 10:26 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] Reminder, CCP4 crystallographic summer school at the APS, June 21 - 29, 2016 Dear Colleagues, This is a reminder that the application deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered. The school will take place from June 21 through June 29, 2016 at the Advanced Photon Source, Argonne National Laboratory, near Chicago. All aspects of macromolecular crystallography from data collection to structure refinement and validation, as well as functional assessment, will be covered. Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts. >From our past experience, the majority of participants bring with them the crystallographic problems they cannot resolve independently and almost all these problems are resolved at the school. Some of the publications, acknowledging the contribution of the school, are listed here: http://www.ccp4.ac.uk/schools/APS-school/publications.php Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue. These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found here: http://www.ccp4.ac.uk/schools/APS-2016/index.php We are looking forward to meeting you in Argonne this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. 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 ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Tuesday, February 23, 2016 7:48 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] CCP4 crystallographic summer school at the APS, June 21 - 29, 2016 Dear Colleagues, We are pleased to announce the 9th 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-2016/index.php Title: CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 21 through 29, 2016 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop the first three 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. Crystallographic computation workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive 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, along with commercial/industrial researchers 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 21. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Registration fees: The registration fee for the selected participants is $400 for the academic and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. 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

9 years, 9 months

[phenixbb] Research Specialist Position at the University of Illinois to Study Ribosome Structure | POLIKANOV Lab

by Yury Polikanov

*Research Specialist Position Available, Department of Biological Sciences, University of Illinois at Chicago - Polikanov Lab* *The Polikanov Laboratory in the Department of Biological Sciences at the University of Illinois at Chicago (IL, USA) is looking for a talented, skillful, and highly motivated researcher to fill the Research Specialist position to study the structure and function of the bacterial ribosome.* For fullest consideration, please submit an application and cover letter describing your scientific interests and how your previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group at https://uic.csod.com/ux/ats/careersite/1/home/requisition/7573?c=uic *Position Summary:* The research in the Polikanov Laboratory at UIC is focused on understanding the basic principles of protein synthesis in bacteria, the modes of action of ribosome-targeting antibiotics, and the mechanisms of drug resistance at a structural level. This position is involved in the determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography and potentially cryo-EM techniques. Expected contributes to the design and delivery of research projects and collaborates with researchers to develop, execute, and interpret research projects. Performs complex laboratory and data collection techniques. *Duties & Responsibilities:* - Perform research relevant to the assigned projects; - Isolate, purify, and crystallize bacterial ribosomes; - Purify all additional components necessary for the crystallization experiments, such as recombinant proteins, tRNAs; - Collect X-ray diffraction data from the ribosome crystals at the APS and NSLS-II Synchrotrons; - Perform structural data analysis; - Coordinate, analyze, and document results for publication; - Directly participate in writing papers and grants based on the experimental data; - Train undergraduate and graduate students in research methods, use of equipment, record keeping, and laboratory database entry; - Attend weekly group meetings and journal club seminars. - Perform other related duties and participate in special projects as assigned. *Minimum Qualifications:* - A bachelor’s degree in chemistry, biochemistry, biophysics, or a related field is required. - A master’s degree in chemistry, biochemistry, biophysics, or a related field is preferred. - A minimum of 3 years related research experience. - Possesses and applies comprehensive knowledge of research principles, concepts, practices, and methods. - Proficient in standard molecular biology and biochemistry lab techniques, such as protein expression, and purification *Preferred Qualifications:* - Experience in structural biology (cryo-EM or X-ray crystallography); - Experience in RNA biology, ribosome, and/or protein synthesis fields. *About the University of Illinois Chicago:* UIC is among the nation’s preeminent urban public research universities, a Carnegie RU/VH research institution, and the largest university in Chicago. UIC serves over 34,000 students, comprising one of the most diverse student bodies in the nation and is designated as a Minority Serving Institution (MSI), an Asian American and Native American Pacific Islander Serving Institution (AANAPSI) and a Hispanic Serving Institution (HSI). Through its 16 colleges, UIC produces nationally and internationally recognized multidisciplinary academic programs in concert with civic, corporate and community partners worldwide, including a full complement of health sciences colleges. By emphasizing cutting-edge and transformational research along with a commitment to the success of all students, UIC embodies the dynamic, vibrant and engaged urban university. Recent “Best Colleges” rankings published by U.S. News & World Report, found UIC climbed up in its rankings among top public schools in the nation and among all national universities. UIC has nearly 260,000 alumni, and is one of the largest employers in the city of Chicago. *The University of Illinois System is an equal opportunity employer, including but not limited to disability and/or veteran status, and complies with all applicable state and federal employment mandates. Please visit Required Employment Notices and Posters <https://www.hr.uillinois.edu/cms/one.aspx?portalId=4292&pageId=5705> to view our non-discrimination statement and find additional information about required background checks, sexual harassment/misconduct disclosures, COVID-19 vaccination requirement, and employment eligibility review through E-Verify. **The university provides accommodations to applicants and employees. Request an Accommodation <https://jobs.uic.edu/request-and-accomodation/>*

2 years, 2 months

Search results for query "look through"