- phenixbb - phenix-online.org

nucleic acid secondary structure restraint sigmas
by Dyda 23 Mar '18

23 Mar '18

Hi, Does anyone one whether is it possible (and if so how) to change the target sigmas of the H-bonds restraining base pairs? It seems that base pair restraints can do several things: base_pair { enabled = True base1 = chain 'C' and resid 21 base2 = chain 'D' and resid 5 saenger_class = 19 restrain_planarity = False planarity_sigma = 0.176 restrain_hbonds = True restrain_hb_angles = True restrain_parallelity = True parallelity_target = 0 parallelity_sigma = 0.0335 What I'd like to know whether the restrain_hbonds and restrain_hb_angles sigmas can be adjusted. Or is it the case that parallelity_sigma is doing what I'm looking for? Thanks! Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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11th CCP4/APS Crystallographic School in the US
by Qingping Xu 22 Mar '18

22 Mar '18

Dear Colleagues, We are pleased to announce the *11th annual CCP4 crystallographic school *“From data collection to structure refinement and beyond” will be held on June 18-25, 2018 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php. *Dates*: June 18 through 25, 2018 *Location*: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: *data collection workshop* and *crystallographic computing workshop*. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop 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 of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). *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 *Wednesday May 2nd, 2018*. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php *Registration fees*: The registration for application is free but there is $500 participation fee for the selected academic students 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 lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

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Fwd: [ccp4bb] Xtriage anomalous signal measurement- mosflm data processing
by Pavel Afonine 22 Mar '18

22 Mar '18

---------- Forwarded message ---------- From: *Manoj Saxena* <00001d16aa30e8a1-dmarc-request(a)jiscmail.ac.uk> Date: Wednesday, March 21, 2018 Subject: [ccp4bb] Xtriage anomalous signal measurement- mosflm data processing To: CCP4BB(a)jiscmail.ac.uk Hi all, I have a dataset for which I got the .sca file from a collaborator and I am trying to look at the strength of the anomalous signal. Looking at archives in the CCP4bb I found many people suggesting using the Chi**2 values using ScaLAPACK using HKL2000. However, at the moment, I have access only to Xtriage from Phenix which gives a clear graph showing that my data has no significant difference anomalous signal. So my question is how reliable is this analysis by Xtriage and is it possible that during data processing anomalous scattering difference was lost. I would like to reprocess the data using mosflm any suggestions for data processing (to see the anomalous signal) would be appreciated. Thanks Manoj Saxena Postdoc University of Puerto Rico

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Phenix.Refine: Missing High Resolution Data
by Mark A. White 16 Mar '18

16 Mar '18

Hello, I have several data sets which seem to loose completeness in their high-resolution shells when the HKL *.sca file is converted into an MTZ. I am using the recommended Diederichs CC1/2 cut off of 0.5, which is usually an I/s <2. I also have an usually high redundancy in these data sets, not sure if that has any effect. Here is a typical comparison of the Phenix statistics and the HKL values. Note that the resolution bins do not match, and that the Phenix refinement was truncated to 3.0Å. PHENIX HKL2000/Scalepack RESOLUTION RANGE COMPL total CC1/2 CC* Redn ScP-Angstrom 50.1353 - 8.8720 97 97.8 0.989 0.997 10.9 70.00 7.87 8.8720 - 7.0483 99 - 7.0483 - 6.1591 100 99.6 0.990 0.997 12.8 7.87 6.25 6.1591 - 5.5968 100 99.7 0.991 0.998 12.9 6.25 5.46 5.5968 - 5.1961 99 - 5.1961 - 4.8900 99 99.6 0.991 0.998 13.0 5.46 4.96 4.8900 - 4.6453 99 99.5 0.986 0.996 12.9 4.96 4.60 4.6453 - 4.4432 99 99.2 0.990 0.997 13.1 4.60 4.33 4.4432 - 4.2723 99 - 4.2723 - 4.1249 99 99.8 0.988 0.997 13.3 4.33 4.11 4.1249 - 3.9960 99 99.9 0.989 0.997 13.4 4.11 3.94 3.9960 - 3.8818 99 99.9 0.987 0.997 13.5 3.94 3.78 3.8818 - 3.7796 100 - 3.7796 - 3.6875 100 99.8 0.985 0.996 13.4 3.78 3.65 3.6875 - 3.6037 100 100.0 0.975 0.994 13.5 3.65 3.54 3.6037 - 3.5270 100 - 3.5270 - 3.4565 100 100.0 0.964 0.991 13.5 3.54 3.44 3.4565 - 3.3912 100 - 3.3912 - 3.3307 97 99.9 0.966 0.991 12.1 3.44 3.35 3.3307 - 3.2742 87 100.0 0.916 0.978 10.2 3.35 3.27 3.2742 - 3.2214 68 100.0 0.857 0.961 8.5 3.27 3.19 3.2214 - 3.1719 54 - 3.1719 - 3.1252 41 100.0 0.763 0.930 7.4 3.19 3.12 3.1252 - 3.0812 33 99.9 0.616 0.873 6.4 3.12 3.06 3.0812 - 3.0396 24 - 3.0396 - 3.0001 18 98.4 0.547 0.841 5.8 3.06 3.00 95.1 0.307 0.685 5.2 3.00 2.95 89.8 0.302 0.681 4.8 2.95 2.90 98.9 0.982 0.995 10.9 All reflect. -- Yours sincerely, Mark A. White, Ph.D. Associate Professor of Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics Macromolecular X-ray Laboratory, Basic Science Building, Room 6.658A University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 mailto://[email protected] http://xray.utmb.edu QQ: "Don’t persist in folly. Some people commit themselves to their errors. They commit one error and consider it constancy to go on that way." - Baltasar Gracian (1658)

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cis-Pro and trans-Pro refinement
by 张士军 16 Mar '18

16 Mar '18

Dear all I am refining a structure which has cis-Pro and trans-Pro, the tans-Pro is gone when I set the "threshold degrees for cis-peptide " from default 45 to 65, but still has cis-Pro. While no significant change when I set it to 15. My question is how to set in phenix refinement in phenix GUI to clear the Pro residues in cis- or trans- conformations. Best Regards shijun

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Phenix refine ligand with alt conf and occupancy<1
by Leonhard Kick 16 Mar '18

16 Mar '18

Dear all, I'm currently working on a structure with a series of ligands which have occupancies of ~80% (according to phenix.refine). So far so good, a few of these also show alternate conformations which I'd like to let phenix refine as well, but phenix.refine adjusts the occupancy of the whole ligand (conformation A+B) automatically to 1. I see that this is useful in most cases, but not in this one. Is there a possibility to adjust the overall occupancy or another work-around that anyone can suggest? Thank you Best Leo -- ================================================== Leonhard Kick AG Schneider Technische Universität München Dept. Chemistry, Chair of Biochemistry Lichtenbergstr. 4 D-85748 Garching b. München +49 89 289 13359 leonhard.kick(a)tum.de ==================================================

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Real space refinement of complete virus structure
by #TOFAYEL AHMED# 13 Mar '18

13 Mar '18

Dear all, I am trying to refine a complete virus pdb structure (possessing icosahedral symmetry) in a cryo-EM map using phenix.real_space_refine. The run fails complaining "Multi-model PDB (with MODEL-ENDMDL) is not supported". So, I followed a previous post in phenixbb: http://www.phenix-online.org/pipermail/phenixbb/2011-May/017079.html and merged multiple models into one but faced following problems: 1. This merged file is unreadable in UCSF Chimera. 2. The secondary structure definition in the PDB file header is not recognizable anymore in Phenix. In my understanding, both the problems are arising due to PDB format's inability to handle more than 62 chains and 99999 atoms in a file. So, what will be the work-around to perform a real space refinement of the complete virus structure at once? Also, how to maintain secondary structure during such refinement? Any help is highly appreciated. Best regards, Tofayel ............................................ Tofayel Ahmed Graduate Student (PhD) | Lab-02n-01 School of Biological Sciences Nanyang Technological University 60 Nanyang Drive, Singapore 637551 +65 8650.0473 |tofayel001(a)e.ntu.edu.sg<mailto:[email protected]>

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AutoSol Br SAD/MAD
by Ian Slaymaker 12 Mar '18

12 Mar '18

Hello Phenixbb, I've been out of the crystallography game for a few years and was hoping for some suggestions. I'm trying to phase a structure (~1200aa protein:DNA complex) with native data out to 2.0A and SAD/MAD data out to 3.0-2.6. I'm trying to use Br/I soaking while I wait for Sel-Met crystals to grow. I'm collecting 1800 frames at a synchrotron and scaling together multiple MAD wavelength sets (30 degree inverse wedges) collected from the same crystal with phenix.scale_and_merge to achieve >85% anomalous data (determined by xtriage). Anomalous signal of the merged data is around 10 at the 3.5 angstrom shell. I'm keeping an eye on the merging statistics, but I'm not sure what the critical stats to monitor are. AutoSol has given me a a few possible solutions, finding between 3 and 8 sites for MAD and SAD sets(I'm letting AutoSol decide how many to find) with Resolve Rfactors around 0.34, but low map skew (<1 and sometimes negative). I've tried using the initial sites to search for additional Br sites, but with no luck, and the density isn't good enough to build anything into. I'm doing hyss searches with various resolution cutoffs and continue to get the same/similar uninterpretable density with very few heavy atom sites found. My questions: What are the critical stats to look at when merging data for anomalous signal? Are there parameters to explore in AutoSol to identify more heavy atom sites? Should I accept that I need to wait for new crystals to grow or keep charging ahead with this data, encouraged by some promising numbers by AutoSol? Thank you in advance for the suggestions. -Ian

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View Solvent Mask
by ben flath 09 Mar '18

09 Mar '18

Hi All I was watching the YouTube tutorial on Polder Maps and noticed that the bulk solvent mask was visualized in coot. How can I visualize my bulk solvent mask? Regards Ben Flath

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Re: [phenixbb] View Solvent Mask
by Flath, Ben 09 Mar '18

09 Mar '18

It seems I am looking for the the compute_box option in polder maps. Ben Sent from my Android -------- Original message -------- From: "Flath, Ben" <bef206(a)mail.usask.ca> Date: 2018-03-09 11:15 AM (GMT-06:00) To: Pavel Afonine <pafonine(a)lbl.gov>, "Flath, Ben" <bef206(a)mail.usask.ca>, phenixbb(a)phenix-online.org Subject: Re: [phenixbb] View Solvent Mask Now the important question How can I modify the mask so it doesn't enter pockets within my model? Add HOH with occupancy set to zero and ignore_zero_occupancy_atoms=False? Or is running polder maps more effective? Thanks again Ben Sent from my Android -------- Original message -------- From: Pavel Afonine <pafonine(a)lbl.gov> Date: 2018-03-09 10:50 AM (GMT-06:00) To: "Flath, Ben" <bef206(a)mail.usask.ca>, phenixbb(a)phenix-online.org Subject: Re: [phenixbb] View Solvent Mask Hi Ben, I was watching the YouTube tutorial on Polder Maps and noticed that the bulk solvent mask was visualized in coot. How can I visualize my bulk solvent mask? phenix.mask model.pdb will calculate the mask. Pavel

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Questions about the Autosol water placing option
by Kaibo Zhang 07 Mar '18

07 Mar '18

Helllo, I was using AutoSol GUI for MR-SAD of my data and trying to turn off "place waters in refinement". However, the output pdb files still got waters in them. I did check the run log file and confirmed both the "place_waters" and the "flood_with_waters" flags were set to false. But in the later session, it still recorded "adding waters in refinement". Is there any parameters I should adjust to avoid adding waters during the Autosol run. Or is it just turned on in the end in order to calculate R_work/free, and doesn't affect your phasing solution? Look forward to your responses. Thank you in advance! Regards Kaibo *Kaibo* PULSe, Purdue University Hockmeyer Hall, Room 321 240 S. Martin Jischke Drive, West Lafayette, IN 47907 Telephone: 765-337-1955 E-mail: zhang644(a)purdue.edu

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Re: [phenixbb] Overlapping ligand-protein side chain density
by van den Bedem, Henry 02 Mar '18

02 Mar '18

If the phe is a gatekeeper, shouldn’t the ligand be refined at partial occupancy; i.e. occupancies not necessarily have to ‘add up’ as you suggest? Maybe this link is helpful too: www.biorxiv.org/content/early/2018/01/24/253419 H From: <phenixbb-bounces(a)phenix-online.org> on behalf of "Phan, Jason" <jason.phan(a)vanderbilt.edu> Date: Wednesday, February 28, 2018 at 1:30 PM To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] Overlapping ligand-protein side chain density All, A piece of a ligand and the side chain of a “gate-keeper” Phe occupy the same space with well-defined features observed for both (resolution is 1.7 A). It looks about 50:50. How do you refine both ligand and protein side chain in this case? A couple of phenixbb suggestions for dealing with ligand-ligand overlapping density have been considered. With the first suggestion, the two entities still clashed and moved apart off of their respective densities. The second suggestion is not applicable in this case since the other molecule is not a ligand but part of the protein but it was tested anyway. Although there was no bumping, the occupancies don’t add up, resulting in a big blob of negative density around the ligand piece. ------------------------------ Only two comments: 1. At that resolution, constrained group occupancy refinement should work reasonably well (provided you can model the 2 entities). Then you also do not have clashes between the molecules, because Occ(A)+Occ(B)=1, meaning when one (A) is there, the other one (B) is not. This works with refmac (external keyword file); if you need more sophisticated occupancy re/constraints SHELXL may offer more opportunities. 2. There is no necessity for the two NCS copies of the binding site to look exactly the same (non-equivalent). Maybe there is a good reason/story (accessibility, contacts etc) for one site to be occupied differently than the other one. Best, BR —————————————— Modeling two molecules that occupy overlapping binding sites in a structure simply involves designating them as alternate conformers, with the same chain and residue number, and an occupancy that sums to 1.0. For example, if you have an AMP and an ADP that occupy the same binding site, you would define them as AAMP B 501 BADP B 501 and initially set the occupancies for the atoms in each conformer to the ratio (50:50, 30:70, etc.) that you observe in the density. Refinement in this manner is straightforward in PHENIX. Diana ----------------------------

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Overlapping ligand-protein side chain density
by Phan, Jason 01 Mar '18

01 Mar '18

All, A piece of a ligand and the side chain of a “gate-keeper” Phe occupy the same space with well-defined features observed for both (resolution is 1.7 A). It looks about 50:50. How do you refine both ligand and protein side chain in this case? A couple of phenixbb suggestions for dealing with ligand-ligand overlapping density have been considered. With the first suggestion, the two entities still clashed and moved apart off of their respective densities. The second suggestion is not applicable in this case since the other molecule is not a ligand but part of the protein but it was tested anyway. Although there was no bumping, the occupancies don’t add up, resulting in a big blob of negative density around the ligand piece. ------------------------------ Only two comments: 1. At that resolution, constrained group occupancy refinement should work reasonably well (provided you can model the 2 entities). Then you also do not have clashes between the molecules, because Occ(A)+Occ(B)=1, meaning when one (A) is there, the other one (B) is not. This works with refmac (external keyword file); if you need more sophisticated occupancy re/constraints SHELXL may offer more opportunities. 2. There is no necessity for the two NCS copies of the binding site to look exactly the same (non-equivalent). Maybe there is a good reason/story (accessibility, contacts etc) for one site to be occupied differently than the other one. Best, BR —————————————— Modeling two molecules that occupy overlapping binding sites in a structure simply involves designating them as alternate conformers, with the same chain and residue number, and an occupancy that sums to 1.0. For example, if you have an AMP and an ADP that occupy the same binding site, you would define them as AAMP B 501 BADP B 501 and initially set the occupancies for the atoms in each conformer to the ratio (50:50, 30:70, etc.) that you observe in the density. Refinement in this manner is straightforward in PHENIX. Diana ----------------------------

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Plots of local real-space CC
by Murpholino Peligro 27 Feb '18

27 Feb '18

Dear all I want to get the values for the blue line (i.e. local real-space CC) in the Molprobity multicriterion plot. How can I do that? I want to plot those values with gnuplot. I do not want the whole graph (red and green lines). Thanks Murphy

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hi please unsubscribe me
by Zhenwei Su 27 Feb '18

27 Feb '18

-- Zhenwei Su 4417 Spruce Street, APT 3A Philadelphia, PA 19104 email: zwsuustc(a)gmail.com cell phone: (608) 698-4156

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hi please unsubscribe me
by Zhenwei Su 27 Feb '18

27 Feb '18

-- Zhenwei Su 4417 Spruce Street, APT 3A Philadelphia, PA 19104 email: zwsuustc(a)gmail.com cell phone: (608) 698-4156

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Issues with refinement of cadmium
by Mohammad Khan 27 Feb '18

27 Feb '18

Dear all, I am trying to fit Cd ion in a protein structure using Phenix. However, the refinement transposes CD to DC and returns me a result with DC ( 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE) in the validation report and gives me the missing atoms accordingly. When I open the same structure in Coot, it shows me the ion Cd. Also, the .pdb file contains Cd. Cd is present in my crystallization condition and fits well into the density. Other metal atoms such as Zn and Cl have refined well. HETATM 5535 CD CD F 1 156.533 -64.594 138.360 1.00 76.11 CD HETATM 5536 CD CD F 2 119.954-111.545 105.562 1.00 35.85 CD HETATM 5537 CD CD F 3 152.936 -93.077 102.747 1.00 28.68 CD HETATM 5538 CD CD F 4 121.467 -96.375 128.574 1.00 72.24 CD Can someone suggest what may be wrong? Thanks in advance!

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[Feature request] Exclude atoms outside user provided mask from refinement (in phenix.real_space_refine)
by Oliver Clarke 26 Feb '18

26 Feb '18

Hi, Often I would like to refine part of a model against a EM map generated by masked refinement. Such a map is typically better than the globally refined map in the region within the mask, and worse outside it. It would be useful to have the capacity to refine the same model first against the globally refined map, and then against the maps generated by masked refinement, but restricting refinement in the latter case to atoms/residues within the bounds of the mask. Is this something that could be maybe added in a future version of phenix.real_space_refine? This would mean allowing the user to provide a mask file, and setting an option to exclude all atoms/residues outside the mask boundaries from refinement. Cheers Oli

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refining a covalent-bound ligand
by Sebastiano Pasqualato 26 Feb '18

26 Feb '18

Hi there, I have a pretty basic question. I am refining a structure in which a drug has been covalently linked to a Cys of the protein. I have generated the .cif fie for the ligand, but I don’t know how to tell the program that carbon C04 has to be covalently linked to the SG of the Cys. Is that sufficient to insert a LINK record in the pdb file? What is the correct syntax for that? Thanks a lot for the feedback and sorry for the naive question, ciao, 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/IEOXtalUnit

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Information regarding Anisotropic atoms
by pooja kesari 22 Feb '18

22 Feb '18

I observed that phenix.refine tool is adding anisotropic atoms to the pdb file by default even at resolution more than 2A. Can anyone please suggest why is it doing so?

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lattice symmetry and free-set selection?
by Edward A. Berry 22 Feb '18

22 Feb '18

Where can I find description of the free-r selection parameters: refinement.input.xray_data.r_free_flags { lattice_symmetry_max_delta=5 use_lattice_symmetry=True } ?

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Industrial Biostructures America 2018 conference
by Leonard,Paul G 20 Feb '18

20 Feb '18

Dear all, The inaugural Industrial Biostructures America conference will be held on 20-22 May 2018 at the Hilton La Jolla Torrey Pines Hotel in San Diego, California. Conference registration and accommodation information is available at: https://industrialbiostructuresamerica.org/ This conference brings together structural biologists from across the pharmaceutical and biotech industry to showcase their cutting-edge research. Scientific sessions will cover the following topics: * Cryo-EM * X-ray crystallography * Lead discovery using NMR * Protein design * Membrane crystallography The Abstract submission deadline is 23rd March 2018. We look forward to seeing you there, Paul Leonard Institute Research Scientist MD Anderson Cancer Center pleonard1(a)mdanderson.org<mailto:[email protected]> The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY
by Salbego, Cyndi 18 Feb '18

18 Feb '18

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. We currently have a number of days open in March. Below is a brief description of our beam lines, and links with more information. The 24-ID-C beamline can deliver X-rays in the range of 6 to 21 keV or ~2.1 to 0.5 Å. This covers most of the popular elemental edges for phasing. This wide energy-range also makes the beamline well suited for ultra high-resolution data collection and soft X-ray sulfur SAD phasing. The beamline is equipped with an optional kappa goniometer for optimal alignment of crystals. A Pixel Array Detector (PAD), Pilatus-6MF, installed on the 24-ID-C beamline helps measure very weak Bragg reflection intensities due to its noise-less readout technology and also provides a very fast data collection capability in shutter-less data collection mode. The 24-ID-E beamline is a fixed energy microdiffraction beamline delivering X-rays at 12.66 keV, optimized for Se-SAD experiments. It is equipped with an Eiger-16M Pixel Array Detector, offering advantages similar to those of the Pilatus-6MF. For more information on our beamlines (beamline and robot manuals): http://necat.chem.cornell.edu To ask about available time please contact Raj Rajashankar (rajashankar(a)anl.gov<mailto:[email protected]>) or Cyndi Salbego (csalbego(a)anl.gov<mailto:[email protected]>) for further information. To apply for General User Time (Rapid Access for current run cycle) please follow this link: https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page Cyndi Salbego Administrator, NECAT 630.252.0689

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9th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 14 Feb '18

14 Feb '18

First announcement 9th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 11 - June 15, 2018 Detailed information: https://conference.sns.gov/biologyneutrons18/ Application deadline: April 30, 2018 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Scattering Scientist, Neutron Sciences Directorate Oak Ridge National Laboratory

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Postdoctoral position in membrane protein structure and function at the NIH
by Anirban Banerjee 13 Feb '18

13 Feb '18

There is an open postdoctoral position for a membrane protein structure-function project in my lab at the NIH. We are currently focusing on integral membrane enzymes (Science. 2018, doi: 10.1126/science.aao6326) and transporters of transition metal ions (J Biol Chem. 2018, doi: 10.1074/jbc.M117.817478). Here is the formal announcement - EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT, BETHESDA, MD AND SURROUNDING AREA Position Description: The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows . The broad interests of the lab are in membrane protein structure and function. We combine structural techniques such as macromolecular crystallography with biophysical and biochemical methods such as reconstitution based assays, high resolution microscopy and small molecule screening to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab has state-of-the-art equipment and facilities. We have dedicated periodic access to the 22-ID beamline at the APS, for crystallographers at the NIH, as well as access to 23-ID and 24-ID beam lines at the APS. Our laboratory is part of the Cell Biology and Neurobiology Branch in the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). We also have an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). Qualifications: The candidates should hold a Ph. D. degree, be author of at least one first author publication and have a strong background in biochemistry or structural biology. Experience with basic molecular biology, protein expression, purification and biochemical characterization are required. Prior experience in membrane protein biochemistry or mammalian expression system for protein purification will be added advantages. It is absolutely essential the candidate is motivated and prepared to put in the best efforts for fruition of the project goals. We are a small, friendly lab and ability to work as part of a cohesive group is important. To Apply: Interested candidates can send an e-mail to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future interests. The NIH is dedicated to building a diverse community in its training and employment programs.

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