- phenixbb - phenix-online.org

Fwd: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB!
by Paul Adams 24 May '13

24 May '13

Begin forwarded message: > From: Gerard DVD Kleywegt <gerard(a)XRAY.BMC.UU.SE> > Subject: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB! > Date: May 24, 2013 11:20:51 AM PDT > To: CCP4BB(a)JISCMAIL.AC.UK > Reply-To: info(a)wwpdb.org > > Dear colleagues, > > I would like to draw your attention to a notification from the wwPDB partners about "Deposition and Release of PDB Entries Containing Large Structures" - see: > > http://www.wwpdb.org/news/news_2013.html#22-May-2013 > > There are major changes afoot in the way large structures are handled in the PDB, as well as in the deposition and annotation procedures and software used by the wwPDB sites. This is of immediate relevance for depositors and users of large structures, but also for software developers and anyone who routinely processes the entire PDB archive or its weekly releases (bioinformatics resources, etc.). From 2014, it will affect essentially everyone who deposits, uses or processes PDB entries. > > If you have any questions about the new deposition system or the procedures for handling large structures or any of the other changes, please contact: info(a)wwpdb.org > > Please pass on this information to anyone likely to be affected by the upcoming changes. Thanks! > > > On behalf of the Worldwide Protein Data Bank, > > --Gerard Kleywegt > > --- > Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK > gerard(a)ebi.ac.uk ..................... pdbe.org > Secretary: Pauline Haslam pdbe_admin(a)ebi.ac.uk -- 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 Building 80, Room 247 Building 978, Room 4126 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 ] --

1 0

Invitation to Participate in a NSF-funded workshop/conference
by Sibo Jiang 24 May '13

24 May '13

Invitation to Participate in a NSF-funded workshop/conference Dear Colleagues in Structural Biology, Recently we have received a NSF grant helping to build the community networks and find solutions for the challenging problems. We have also discussed with the program officer of US National Science Foundation on planning for a research conference/workshop series proposal to US NSF. This conference/workshop series will particularly focus on the technical issues and practical challenges in structural biology of nucleic acids, protein-nucleic acid complexes and small molecule-nucleic acid complexes. These challenges include crystallization, derivatization, phasing and high-resolution structure determination. You are invited to participate in this conference/workshop series. If you are interested in our invitation, please reply this email or send your email to huang(a)gsu.edu<mailto:[email protected]>. In your email, please let us know your name, research interests (up to five key words), affiliation and phone number. The details will be announced later. Colleagues in academia are encouraged to forward this email to your friends and colleagues in industry. Colleagues in industry are particularly welcome. Sincerely, The Planning Committee of the NSF-funded Conference/Workshop

1 0

FW: need suggestion
by afshan490＠yahoo.com 24 May '13

24 May '13

<br/><br/><br/>Sent from Yahoo! Mail for iPhone

2 1

From Dmitri Svergun and Matthias Wilmanns: 11th International Conference: Biology and Synchrotron Radiation (BSR)
by Terwilliger, Thomas C 24 May '13

24 May '13

11th International Conference: Biology and Synchrotron Radiation (BSR) 8-11 September 2013, EMBL Hamburg, Germany Abstract submission deadline is approaching – 1st June 2013! Join us in Hamburg, Germany for BSR 2013! Scientists at all possible career levels are invited to this meeting. Check out our preliminary programme to learn more! http://www.bsr2013.org/BSR13-01/programme/index.html Young researchers are highly welcome to apply for a travel grant from the International Union of Crystallography when registering. http://www.bsr2013.org/BSR13-01/info/index.html Present your work! Selected talks and poster sessions provide great opportunities for participants to present their work. Unique networking opportunities are also available to meet colleagues, friends and future collaboration partners from all over the world. Discover the city of Hamburg! BSR 2013 includes a social programme with boat trips and day and night excursions. Accompanying persons will enjoy special rates! http://www.bsr2013.org/BSR13-01/attractions/index.html A tour of DESY’s most impressive research infrastructures - including PETRA, FLASH and the future X-FEL – is included in the registration fee. http://www.bsr2013.org/BSR13-01/desy/index.html Dates at a glance: · Registration and abstract submission: 1 June 2013 · Registration without abstract: 1 August 2013 Take a look at the updated BSR webpage (www.bsr2013.org<http://www.bsr2013.org>) for more information and to register. CONTACT Diah.Yulianti(a)embl.de<mailto:[email protected]> Alternatively, contact us on the event facebook page https://www.facebook.com/events/332259356868854/

1 0

Call for Proposals: IMAGINE, a New Neutron Crystallography Diffractometer
by Meilleur, Flora 23 May '13

23 May '13

IMAGINE, Neutron Crystallography Diffractometer High Flux Isotope Reactor (HFIR), Oak Ridge National Laboratory Call for proposals for experiments anticipated to run from August through December 2013 You are invited to apply for beam time on the neutron quasi-Laue diffractometer IMAGINE, at the High Flux Isotope Reactor. Proposal will be accepted via the web-based proposal system until NOON Wednesday, July 31, 2013. This call is for experiments anticipated to run from August through December 2013. Please see the attached flyer for additional information. For technical information about the capabilities of IMAGINE go to neutrons.ornl.gov/imagine/<http://neutrons.ornl.gov/imagine/> or contact Flora Meilleur, meilleurf(a)ornl.gov, or Andrey Kovalevsky, kovalevskyay(a)ornl.gov. Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University IMAGINE lead scientist, Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

1 0

conflicting bond_simple restraints
by Jianxun Qi 23 May '13

23 May '13

Hi, I had a phosphoserine (SEP) in my structure that is attached in this message. The data_link file for SEP already exists in the mon_lib (data_link_SEPC-N) and the corresponding cif_link I used is as follow: refinement.pdb_interpretation { apply_cif_link { data_link = "SEPC-N" residue_selection_1 = "chain C and resname PHE and resid 3" residue_selection_2 = "chain C and resname SEP and resid 4" } apply_cif_link { data_link = "SEPC-N" residue_selection_1 = "chain C and resname SEP and resid 4" residue_selection_2 = "chain C and resname ARG and resid 5" } } When I run the phenix.refine (my version is phenix-1.8-1069), it said conflicting bond_simple restraints: Sorry: Conflicting bond_simple restraints: 1. definition from: residues: PHE + SEP 2. definition from: residues: PHE + SEP atoms: "ATOM 3121 C PHE C 3 .*. C " "ATOM 3192 N SEP C 4 .*. N " Has anyone ever experienced this case before? Any hints are welcome. Regards Jianxun Qi May 22,2013

2 1

Ca occupancy in multiple soaked structures
by Daniel Slade 23 May '13

23 May '13

Hi Everyone, I have a complex case of data analysis I would love some opinions on. I have a group of structures of a protein that binds 6 calciums, and we want to know the order/concentration at which they fill. The crystals were soaked with calcium from 0-10 mM and all are 1.6-2.1 A in resolution. I determine the order of the calcium binding, and now I am working on the percent occupancy at each concentration. To do this, I have removed the calciums, and then performed simulated annealing for each structure from 2.1-30A resolution to 'normalize' them. I then look at the omit map and scroll out to find the peak sigma intensity of where the calciums should be. The curves fit very well for each calcium, and the numbers correspond well with other solution studies we have. My thought is that I need to normalize this in another way, so I thought choosing a water molecule that is present in all of the structures and removing it, then performing simulated annealing would be a good idea to normalize the peak intensity for each calcium soak concentration, since this water molecule shouldn't change occupancy. Is this the proper way to do this, or can you guys suggest a better way to go about this. I also looked at B factor and e/A3, but that isn't as consistent as peak sigma. Thanks in advance. Dan Daniel J. Slade, Ph.D. Research Associate Thompson Lab The Scripps Research Institute 130 Scripps Way Jupiter, FL 33458 (561) 228-3213

4 3

43rd Mid-Atlantic Macromolecular Crystallography Meeting -- reminder
by Charles Pemble 22 May '13

22 May '13

*43**rd** Mid-Atlantic Macromolecular Crystallography Meeting* *May 30 – June 1, 2013* *Duke University* *Durham, NC* This is a reminder for the 43rd Mid-Atlantic Macromolecular Crystallography Meeting, which will be held next week, May 30-June 01 at Duke University in Durham, North Carolina. Registration and details can be found at http://www.mid-atlantic.org. We encourage you to submit your abstracts for a poster presentation as the deadline is fast approaching! *DEADLINES (updated):* Abstract submission for poster - Next Monday, May 27th *No deadline for registration With best wishes on behalf of the primary Organizing Committee, Charlie Pemble _____________________________ Charles W. Pemble IV, Ph.D. Duke University Medical Center 308 Research Drive LSRC, A06 Durham, NC 27708 charles.pemble(a)duke.edu We thank our current sponsors for their generous contributions: Rigaku Americas Corporation, Agilent Technologies Inc., GlaxoSmithKline, Art Robbins, Bruker, HKL Research Inc., Molecular Dimensions, Hampton Research, Labcyte, GenScript, Genentech, Emerald BioSystems, TTP LabTech, Oxford Cryosystems, PhD Posters, Duke University School of Medicine, Duke Human Vaccine Institute, and Avanti Polar Lipids Inc.

1 0

Workshop - The Future of Microfocus Protein Crystallography - 24-25 September, 2013, Lund, Sweden
by Marjolein Thunnissen 22 May '13

22 May '13

Dear all, I would like to announce a workshop on "The Future of Microfocus Protein Crystallography" which will take place at the MAX IV User meeting on the 24th and the 25th of September, 2013, in Lund, Sweden. Recent developments within protein crystallography methods in combination with the possibilities offered by the new upcoming synchrotron sources such as the MAX IV 3 GeV storage ring make possible exciting new ways of carrying out research within structural biology. Small microfocus beamlines with a very high flux and increased coherence will make new types of experimentation possible. The scientific possibilities will be highlighted through a series of talks by experts showing the impact of the new type of X-ray sources and microfocus beamlines on research within structural biology. The new generation of microfocus beamlines will also set a high demand on instrumentation and suitable software. For example, data collection will potentially be very fast (in milliseconds) and radiation damage will allow only a limited amount of data to be collected from each sample. New technical solutions for sample handling and presentation, data processing methods and more will be needed for these types of experiments, and these will also be presented and discussed at the workshop. Confirmed speakers include David Stuart, Daniel Wacker, Simone Weynand, Jens Preben Morth, Tove Sjögren, Richard Neutze, Janet Smith, Alke Meentz, Alexei Soares, Thomas White and Clemens Schulze-Briese The workshop is part of a process to obtain an updated proposal for the possible Phase 2b beam line MicroMAX at the upcoming new 3 GeV storage ring of MAX IV in Lund. This workshop should give the user community an opportunity to explore the scientific possibilities of a new generation of microfocus beam lines, but also it will give them the chance to contribute with specific input on their own experimental demands on the beam line. The workshop is part of the MAX IV laboratory user meeting. Registration will be through the user meeting website which will open for registration soon. Further information on this workshop can be found at https://www.maxlab.lu.se/node/1609 and for the MAX IV user meeting at https://www.maxlab.lu.se/um13 . For the organisers, Richard Neutze, Gunter Schneider and Gregers Rom Andersen Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

1 0

depositing pdb files
by Mengbin Chen 21 May '13

21 May '13

Hi Phenix Users, I am going to deposit some pdb files into RCSB, which requires Luzzati plots and a bunch of other things. I don't know how to get these results from Phenix (actually the main problem is luzzati errors, Phenix does not seem to provide them), although SFcheck from CCP4i provides only some of them. I know CNS can do this by model_stats.inp, but that's too much trouble since I have complicated ligands bound. Any suggestions would be appreciated! Thank you in advance, Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

4 5

mr_rosetta: how to continue from recovered mr_protocols.default run
by Christian Becke 21 May '13

21 May '13

Hi, I am trying mr_rosetta on a complex. At the GROUP_OF_ROSETTA_REBUILD stage, my machine ran out of memory and the mr_protocols.default processes were killed. After adding more swap space, I restarted the mr_protocols.default runs (3 parallel jobs, one for each chain) using the scripts RUN_?/WORK_?/run_rebuild.sh, which appear to have finished correctly (i.e., there are 20 pdb files generated for each of the chains). However, I could not figure out how to restart mr_rosetta so that it picks up these models. Any suggestions? Thanks, Christian

2 1

Grid size in max_entropy maps
by Schubert, Carsten [JRDUS] 20 May '13

20 May '13

Is there a way to control the grid size in the maximum entropy maps? The current grid size is quite small, resulting in a very fine mesh. Thanks Carsten

3 5

43rd Mid-Atlantic Macromolecular Crystallography Meeting
by Charles Pemble 11 May '13

11 May '13

*43**rd** Mid-Atlantic Macromolecular Crystallography Meeting* *May 30 – June 1, 2013* *Duke University* *Durham, NC* *ANNOUNCEMENT: *We have extended the deadline for submitting abstracts to be considered for presentations until midnight Sunday, May 12. Registration and details can be found at http://www.mid-atlantic.org. The 43rd Mid-Atlantic Macromolecular Crystallography Meeting, will be held at Duke University in Durham, North Carolina. This year will feature keynote speaker Tom Terwilliger from Los Alamos National Lab, workshops on PHENIX and MolProbity, plus many talks & posters on new and exciting research. The best presentation and poster by a Graduate Student & Postdoctoral Fellow will be awarded (total of 4). We encourage you to submit your abstracts and sign up for the workshops as these are separate processes from registration. *DEADLINES (updated):* Abstract submission for presentation - May 12th Abstract submission for poster - May 27th *No deadline for registration With best wishes on behalf of the primary Organizing Committee, Charlie Pemble _____________________________ Charles W. Pemble IV, Ph.D. Duke University Medical Center 308 Research Drive LSRC, A06 Durham, NC 27708 charles.pemble(a)duke.edu We thank our current sponsors for their generous contributions: Rigaku Americas Corporation, Agilent Technologies Inc., GlaxoSmithKline, Art Robbins, Bruker, HKL Research Inc., Molecular Dimensions, Hampton Research, Labcyte, GenScript, Genentech, Emerald BioSystems, TTP LabTech, Oxford Cryosystems, PhD Posters, Duke University School of Medicine, Duke Human Vaccine Institute, and Avanti Polar Lipids Inc.

1 0

Submissions for next CCN newsletter
by Nigel Moriarty 07 May '13

07 May '13

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the June 2013 issue is 31 May, 2013 but if you can send me drafts before the 15th of May we can get started on generating proofs. 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

1 0

43rd Mid-Atlantic Macromolecular Crystallography Meeting
by Charles Pemble 07 May '13

07 May '13

*43**rd** Mid-Atlantic Macromolecular Crystallography Meeting* *May 30 – June 1, 2013* *Duke University* *Durham, NC* This is a reminder for the 43rd Mid-Atlantic Macromolecular Crystallography Meeting, which will be held at Duke University in Durham, North Carolina. This meeting fosters discussion and interaction among structural biologists from around the Mid-Atlantic region. Registration and details can be found at http://www.mid-atlantic.org. The deadline for registration is May 15th. This year will feature keynote speaker Tom Terwilliger from Los Alamos National Lab, workshops on PHENIX and MolProbity, plus many talks & posters on new and exciting research. Presentations will be selected from submitted abstracts and preference will be given to young researchers. The best presentation and poster by a Graduate Student & Postdoctoral Fellow will be awarded (total of 4). We encourage you to submit your abstracts and sign up for the workshops as these are separate processes from registration. *DEADLINES:* Registration - May 15th Abstract submission for presentation - May 10th Abstract submission for poster - May 27th *IMPORTANT: *A block of rooms have been reserved at the Millennium hotel as well as the Duke dormitories. The deadline for reserving a room at the Millennium is May 9th. With best wishes on behalf of the primary Organizing Committee, Charlie Pemble _____________________________ Charles W. Pemble IV, Ph.D. Duke University Medical Center 308 Research Drive LSRC, A06 Durham, NC 27708 charles.pemble(a)duke.edu We thank our current sponsors for their generous contributions: Rigaku Americas Corporation, Agilent Technologies Inc., GlaxoSmithKline, Art Robbins, Bruker, HKL Research Inc., Molecular Dimensions, Hampton Research, Labcyte, GenScript, Genentech, Emerald BioSystems, TTP LabTech, Oxford Cryosystems, PhD Posters, Duke University School of Medicine, Duke Human Vaccine Institute, and Avanti Polar Lipids Inc.

1 0

Morphing only a part of the model?
by Guenter Fritz 06 May '13

06 May '13

Dear all, I am working on a multisubunit protein complex (ca. 2000 residues). I would like to morph only a part or one subunit into the experimental electron density without morphing the rest of the protein. iIs there a way to select a subunit or a part of the model? Best regards, Guenter

2 3

Find Difference peaks and holes
by John Rose 03 May '13

03 May '13

Hi, I can't seem to find the "Find Difference peaks and holes" utility in the PHENIX 1.8.2-1309 distribution. I found it to be very useful. Can you tell me where it is hiding. Regards, John John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 ========================================= Phone: 706-542-1750 Fax: 706-542-3077

4 4

ReadySet & phenix.refine problem: NAG-Asn with hydrogen atoms
by Zhijie Li 30 Apr '13

30 Apr '13

Hello, I am refining my structure with hydrogen atoms on (phenix 1.8.2-1309). The protein contains two Asn-linked GlcNAc. I noticed two problems with respect to the NAG-Asn linkage in the presence of hydrogen atoms: 1) After running ReadySet (to add hydrogen to the PDB ab initio), the H1 on the NAG is pointing to the amino group of Asn, ie, the NAG seems to be interpreted as in its alpha anomer instead of beta (should be GlcNAc beta1,N-Asn). This is not really a problem as it doesn't seem to affect the refinement. 2) The H21 in Asn is correctly removed by ReadySet, leaving only H22. However, if I send this PDB to phenix.refine, the refinement will fail almost instantly complaining that H22 of the Asn has an unknown nonbonded energy type symbol. But if I simply change the atom name of H22 to H21, the refinement will proceed to completion with no problem, only leaving an H21 at the position where H22 should be. I was not sure what caused this error. So I trimmed my PDBs down to the Asn and NAG only, and fed the small PDB to ReadySet and phenix.refine (with an eff file indicating the NAG-Asn linkage) and got the same behavior: H22 on Asn - error; H21 on Asn - OK. I hope someone can look into this. Thanks in advance. Zhijie

2 3

SIGF in refinement
by Aksyuk, Anastasia (NIH/NIAMS) [F] 29 Apr '13

29 Apr '13

Hi, I was wondering how SigFobs values are used in phenix refinement and how important those are. I am asking in view of P1 space group with low redundancy or even cryo-EM map based Fobs. Maybe you can point me to a useful reference on likelihood targets. I feel lost in those that I have. Thanks, --Anastasia ------------------------------ Anastasia A Aksyuk, PhD Laboratory of Structural Biology, NIAMS Bldg 50, Room 1511, 50 South Drive MSC 8025 N.I.H., Bethesda, MD 20892-8025 tel 301 451-8247 e-mail: anastasia.aksyuk(a)nih.gov

2 1

Re: [phenixbb] clashscore discrepancies
by Alex Theodossis 28 Apr '13

28 Apr '13

Dear phenixbb, I have carried out refinement using the latest version of PHENIX, which gives improved molprobity stats. However, these stats still do not match those porvided by the molprobity server: PHENIX output Molprobity server Existing H-model Electron-cloud H-model All atom clashscore 2.57 4.2 (81st perc) 3.25 (88th percentile) Rotamer outliers 0.7 1.14 1.14 Overall score 1.04 1/24 (89th perc) 1.16 (93rd percentile) Given that PHENIX is now giving me the best results and all scenarios give reasonable results I am less inclined to be concerned. However, I still find these inconsistencies rather puzzling and am curious to learn what is causing them. Thanks in advance.

3 2

phenix.elbow: Best ploy to generate restraints files for similar compounds ?
by Phil Jeffrey 26 Apr '13

26 Apr '13

I've got homologues of small molecule compounds I want to generate restraints for. The changes I'm looking at are converting O to S and moving a substituent around on a phenyl ring. I expect them to have similar conformations overall. Is the best method to: 1. create a new PDB file of the homolog, change atom types and do some primitive modeling, assuming that the --opt method will fix geometry snafus ~or~ 2. use a SMILES string, edit the numbering of the PDB file and regenerate the restraints from that Thanks Phil Jeffrey Princeton

2 1

clashscore discrepancies
by Alex Theodossis 25 Apr '13

25 Apr '13

Dear phenixbb, Have refined a 1.05A structure with riding hydrogen model in phenix v1.8.1-1168 and doing final validation. The molprobity statistics output by phenix include: all atom clashscore = 4.12 Rotamer outliers = 0.71% Overall score = 1.2 Put through the molprobity server I am given the option of analysing with existing hydrogen model, or replacing with the 'electron-cloud parameters' they recommend for X-ray crystal structures. The results end up being very different: existing H model: electron-cloud model: All atom clash score: 4.66 (78th percentile) 3.72 (85th percentile) Poor rotamers: 1.14% 1.14% Overall score: 1.28 (88th percentile) 1.20 (92nd percentile) While all three scenarios give acceptable statistics, I am surprised by the inconsistency in the results given by molprobity, even when using the same hydrogen model. I am also wondering whether I am using a suboptimal riding model in my refinement (generated using phenix ready-set). Can anyone advise on the reason for these inconsistencies (is it just due to differences in the version of molprobity being run in each case). Is there anything I should be doing differently? Thanks in advance. On 18 November 2012 12:36, Alex Theodossis <alex.theodossis(a)monash.edu>wrote: > Hi, > > I'm attempting to install the latest version of phenix on mac 10.5.8, > using the command line installer. > > Installation proceeds well until towards the end, where it hangs on: > > precompiling .py files > > I can leave it for up to an hour without any further progress, but upon > typing: > > ctrl+c > > The installation comes back to life and proceeds to completion. > > Can anyone advise as to what might be causing this and on how reliable > this installation is going to be? > > Thanks in advance. > > >

3 2

Postdoctoral positions in structure and function of membrane proteins at the NIH
by Anirban Banerjee 25 Apr '13

25 Apr '13

Dear all, Will you please bring this to the attention of suitable candidates ? Postdoctoral positions in structure and function of membrane proteins at the NIH The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows to start from September, 2013 or later. The broad interests of the lab are in membrane protein structure and function. We will combine macromolecular crystallography with functional assays with detergent-solubilized and liposome-reconstituted proteins to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab is part of the Cell Biology and Metabolism (CBMP) program and is part of a large and diverse macromolecular crystallography and NMR community in the NIH campus. There is ample opportunity to interact with other scientific groups across a broad range of scientific disciplines. CBMP is part of the National Institute of Child Health and Human Development (NICHD). Our lab also has an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). The DC Metro area is a wonderful place to live, the weather is pleasant and the NIH is a vibrant international community. Candidates must be motivated and have a strong background in biochemistry and structural biology. Experience with protein expression, purification and crystallization is required. Prior experience in membrane protein biochemistry will be an added advantage. Candidates should hold a Ph.D. degree by the time they join and have no more than one year of postdoctoral experience at the time of applying. To apply, please send an email of interest to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future research interests. Best regards, Anirban

1 0

install problem on Ubuntu 12.10
by Guan Hong Hsiang 25 Apr '13

25 Apr '13

Dear all: When I wanted to install phenix on my computer with ubuntu 12.10 (./install), the error message showed that "/usr/local/phenix-installer-1.8.2-1309/bin/install-from-binary:130:export:6 core : bad variable name. I am a newbie of phenix. Could anyone give me some suggestion? Thank you Hong-Hsiang

2 4

phenix.refine - blocking sorry error
by Maxime Cuypers 24 Apr '13

24 Apr '13

hello, i just installed the latest buid of phenix : 1356 i now get the following error in phenix.refine - this was ok with previous version ' Sorry: Your refinement strategy includes anisotropic ADPs for hydrogen atoms refined individually; hydrogens should be left as isotropic even for individual refinement. ' which is the new specific command to add to the .params file that will force anisotropic refinement of deuteriums please? PS: this is needed for my neutron structure refinement. thanks for your help -- Dr. Maxime Cuypers Institut Laue Langevin (ILL), Deuteration lab Rue Jules Horowitz, 6, BP 156 38042 Grenoble cedex 9 France

2 1