- phenixbb - phenix-online.org

protein atom selection
by wtempel 04 Feb '17

04 Feb '17

Hello all, in my hands and to my surprise, PHENIX atom selections such as "protein" or "peptide" would include a co-factor like SAM. Did others notice that also? Is this behavior what most users would want or even expect? Best regards. Wolfram Tempel

4 5

Refine a structure with a disconnected region
by Yasser Almeida Hernández 02 Feb '17

02 Feb '17

Hi all, I am refining a structure at 1.9A, which contains a 7 residues C-terminal region. The resolution of the map in that region is low but is clear enough to define some side chains and the backbone. I build this region manually in Coot. This region is disconnected from the core of the protein, since the connecting loop cannot be seen in the density map. After running phenix.refine (GUI) and playing with the options several times, the final model of this region is always out of the map, even when the R values are improved. How can I refine the structure, keeping that part of the protein in its place, fitted to the map? Thanks in advance Best Yasser

2 1

10th CCP4/APS Crystallographic School in the USA
by Sanishvili, Ruslan 02 Feb '17

02 Feb '17

Dear Colleagues, We are pleased to announce the 10th annual CCP4 crystallographic school “>From data collection to structure refinement and beyond”, held at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php Dates: June 19 through 26, 2017 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop: 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 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 April 19. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2017/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, lodging and breakfast. 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

1 0

Announcement: Phenix tutorial videos
by Dorothee Liebschner 01 Feb '17

01 Feb '17

Dear Phenix users, Video tutorials about Phenix tools are now available on the Phenix Tutorial YouTube channel <https://www.youtube.com/channel/UCcdI0hfHngWAZLJWynxPQWg>. The videos give a short introduction about a Phenix tool, summarize the required input files and parameters, explain how to run it and – when appropriate – discuss the results. So far, the following topics are covered: - How to run phenix.refine - How to calculate polder maps - How to run phenix.real_space_refine - How to run PDB tools - How to change phenix.refine parameters via the GUI More videos will be added in the future. Feedback about the videos is very welcome (tutorials(a)phenix-online.org - or use the comment section on YouTube). If you are eager to see a tutorial about a certain (Phenix-related) topic, don't hesitate to tell us: tutorials(a)phenix-online.org. Also, if you want to make your own Phenix tutorial and publish it on the channel, get in touch with us. Further info: To see subtitles, hit the cc (closed captions) button in the right bottom of the video screen. Subscribe to the channel to see the tutorial videos in your YouTube subscription feed. To get notifications about new videos, tap the bell button (next to the "subscribe" button). Best wishes, The Phenix team

1 0

Creating custom peptide bonds
by Pearce, N.M. (Nick) 01 Feb '17

01 Feb '17

Hi, I have a rather odd model situation, where I’m trying to manually create peptide bond restraints between two alternate conformers in refinement. I’m doing this using: ======= ... refinement.pdb_interpretation.apply_cif_link { data_link = TRANS residue_selection_1 = chain "A" and resid " 38 " and altid "B" residue_selection_2 = chain "A" and resid " 39 " and altid "C" } refinement.pdb_interpretation.apply_cif_link { data_link = TRANS residue_selection_1 = chain "A" and resid " 38 " and altid "B" residue_selection_2 = chain "A" and resid " 39 " and altid "D” } ... ======= However, running phenix.refine with this I get the error: ======= RuntimeError: Unused apply_cif_link: TRANS ['pdbres="MET A 38 "', 'pdbres="GLU A 39 “'] ======= Given that the alternate conformers have been removed from the labels, I assume that this can only be used to define links between residues, but not between specific conformers? Is there any way to do this? Thanks, Nick Nicholas Pearce Post-doctoral researcher Universiteit Utrecht

2 1

omit map problems
by Thomas, Leonard M. 01 Feb '17

01 Feb '17

Okay this is a bit frustrating. Trying to run a simple omit map. Have a mtz file used for refinement and the out pdb file from refinement and every time I try to run the script it comes up with No PDB file defined error. Check both files and they appear fine. System is a Mac-Pro running Sierra. Thanks in advance. Leonard M. Thomas Ph.D. Macromolecular Crystallography Laboratory Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology Department of Chemistry and Biochemistry University of Oklahoma Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019 405-325-1126 lmthomas(a)ou.edu http://barlywine.chem.ou.edu http://structuralbiology.ou.edu

3 2

Time to submit abstracts for ACA 2017 (May 26-30 in New Orleans)
by Terwilliger, Thomas Charles 31 Jan '17

31 Jan '17

Dear Friends and Colleagues! Mark your calendars and join us in May for the 67th Annual Meeting of the American Crystallographic Association (ACA), to be held May 26-30 in New Orleans, LA, at the Hyatt Regency Hotel. The abstract submission is opened now till February 15th. http://www.amercrystalassn.org/2017-meeting-homepage Back by popular demand - New Orleans ACA Meeting T-shirts with designs on the front and back. Don't be a square and get yours today. Hurry! They can be pre-ordered during the registration or at direct link: https://www.booster.com/aca-meeting-in-new-orleans The meeting will launch with a full day of workshops<http://www.amercrystalassn.org/2071-main-workshops> on four different topics followed by an Opening Ceremony with a plenary lecture by Sir James Fraser Stoddart, 2016 Nobel Laureate in Chemistry. The theme of this year's Transactions Symposium is Cryo Electron Microscopy that will feature lectures by the world's leading researchers and experts. New this year will be a session on NMR crystallography. Both are dedicated to covering topics of importance to scientists with a wide range of professional backgrounds and designed to emphasize our need for collaboration and cooperation. Young researchers<http://www.amercrystalassn.org/2017-young-scientists> will benefit from special and free events such as Career Development, Networking Mixer, Diversity and Inclusion, Communicating Science to Public, Undergraduate Research Symposium as well as educational sessions and workshops. You are encouraged to apply for funding support through travel grants before February 15th, by volunteering, or just contact us if you are many students coming from the same lab. Best regards, Tom T Tom Terwilliger ACA Past President

1 0

question in geometry refinement
by Noelia Bernardo García 26 Jan '17

26 Jan '17

Dear colleagues, I am dealing with the refinement of a protein with 5 monomers in the asymmetric unit at 2.2 Å resolution. Four of them have correct geometry and good density map, however, the fifth molecule has poor density and bad geometry. Ramachandran plot is presents 91.05% (favored), 3.23 % (outliers). I have modified the occupancy of the molecule, the refinement results in 0.8 occupancy for this chain. I also tried to refined the structure without this chain, but the R values increased and the density map indicated that it should be there. I would like to refine this chain fixing the geometry of the others which are correct. Do you have any ideas about how to proceed? Some info: Protein residues 305 5 monomers in the a.u Space group C121 a=151.390, b= 67.81, c=155.420Å, 94.53º R value 0.23 / Rfree 0.28 Many thanks, Noelia Noelia Bernardo García, PhD Instituto de Química Física "Rocasolano" Spanish National Research Council (CSIC) c/ Serrano 119 28006 Madrid (Spain) Phone: +34-91 561 94 00 (ext. 961107) e-mail: xnoelia(a)iqfr.csic.es

2 1

on graphical interface of Phenix 1.10.1-2155-000
by johnpontty＠yahoo.com 25 Jan '17

25 Jan '17

Dear All, For the "refinement settings" in the phenix.refine graphical interface, will you please let me know when we need to change the parameters in "Refinement target weight..."? And is any rule on how to modify the parameters in "Refinement target weight..."? John

2 1

multi-domain protein data, and multi-component/full-featured Phaser-MR
by Emilia C. Arturo (Emily) 23 Jan '17

23 Jan '17

Hello. I have been reading the tutorials and the 2007 McCoy (Acta D) paper about how to use the full-featured Phaser-MR tool (with the Phenix GUI) to do MR. I am struggling with how to define the Ensembles, and the Search procedure. Specifically, after setting up the Ensembles and the Search procedure, as I'd deduced that they should be done, I ran the script and get the following message: >>Search request requires more scattering than defined in composition. Composition increased to accommodate search components.<< I guess that I have not understood how to set up the multi-component search to do what I want for it to do: I'd wanted the tool to search for the best placement of individual domains, given a set of diffraction data and a collection/combination of pdb files that contains coordinates for individual domains. This is the context: The diffraction data is from a crystal of a three-domain protein. The first model I used for MR was a crystal structure of the largest of these domains, which had been expressed and purified alone. With this one domain as a search model (using the single-component Phaser-MR) I obtained a solution without a problem, but now have density into which I will need to place the other two domains. The second-largest domain has also been crystallized (also on its own). Its structure (as a monomer or dimer) is available from different organisms, some dimers engage different inter-chain interfaces, and some have ligands bound at different interfaces. There does exist a crystal structure for the three-domain protein, and its biological assembly is 4. I have reason to think that this new crystal is of this same protein in a different configuration - that is, in this crystal structure the three domains are oriented differently to one another than they were in the first 3-domain structure. In solution this protein can be a dimer or tetramer. The ASU for this dataset is 2 chains, and I assume that each chain has all three domains intact. This diffraction data is of relatively poor resolution (~3.8A). So, I configured the Phaser-MR run as follows, using the AP2 and Beta-blip case studies as examples: - In the 'Ensembles' tab I created 17 different ensembles, each with a different combination of single-domain structures (or with just the single largest domain, as in the original MR single-component search). - In the 'ASU contents' tab I provided the sequence of the full-length (3-domain) protein, and set 'Number of copies' to 2. - In the 'Search strategy' tab I added each of the 17 Ensembles as a separate 'Component' with 'Copies to search for' set to 2. This seems redundant to what I'd put in to the 'Ensembles' tab. I thought that a 'component' meant a single pdb file representing a single chain or domain (in this case) while an 'Ensemble' meant a collection of components so that, e.g., a 3-domain chain could be described as an ensemble of 3 components. Do you have advice on how to set up this search correctly? Regards, Emily. -- "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May Alcott

1 0

phenix.find_blobs command problems
by oleg＠quantumbioinc.com 20 Jan '17

20 Jan '17

I tried to use phenix.find_blobs command but it ended up with a Python crash. Any thoughts? Thanks a lot Oleg P.S. I tried to attached the input files but it seems to be over the allowed message size phenix.find_blobs protein_pdb_file_name=1LRI-H_refine_001.pdb map_coeffs_file_nam=1LRI-H_refine_001.mtz #phil __OFF__ banner #phil __ON__ find_blobs { input { protein_pdb_file_name = "1LRI-H_refine_001.pdb" data_file_name = None map_coeffs_file_name = "1LRI-H_refine_001.mtz" } output { blob_number = None } options { random_seed = 0 density_contour = 2.5 } } #phil __END__ Random number seed: 3628800 Adding PDB model from 1LRI-H_refine_001.pdb Traceback (most recent call last): File "/home/oleg/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/find_blobs.py", line 169, in <module> run( tuple(args) ) File "/home/oleg/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/find_blobs.py", line 162, in run rc = execute(params) File "/home/oleg/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/find_blobs.py", line 98, in execute bfo.setup_blobs(working_params.options.density_contour) File "/home/oleg/phenix-1.11.1-2575/modules/phenix/phenix/ligands/blob_finding_class.py", line 25, in setup_blobs contour=contour, File "/home/oleg/phenix-1.11.1-2575/modules/phenix/phenix/ligands/DensityBlobsClass.py", line 14, in __init__ self.map_residue = self.data_map["fofc_fft_map"] # fft map TypeError: 'fft_map' object has no attribute '__getitem__'

1 0

on use of pdbtools
by Smith Liu 20 Jan '17

20 Jan '17

Dear All, Can you show me how to use the phenix pdbtools to get the mate pdb of the original input pdb?Take the phenix pdbtools graphical interface for example, I think after I load the original pdb, I should click "options" and then click "Coordinates". Suppose my original PDB was X, Y, Z, and I want to get the mate PDB -X +Y, -X ,1/3 +Z, then how should I input the "Switch rotamers", "Translate", and "Rotate" for this specific example? Does it has anything to do with "Euler angle convention"? I am looking forward to getting a reply from you. Smith

1 0

polder vs fem vs composite omit map vs maximum entropy
by Murpholino Peligro 20 Jan '17

20 Jan '17

So I got a MR solution and maybe a dozen residues are not clearly defined (most of them in the surface) I used to compute the feature enhanced map but now I can see there are a lot of options in phenix->maps. Which one is better for me? (~130 residues, 1.5 A resolution, ~ 90% complete) Probably I should try them all, and compare them visually in coot with appropiate sigmas (taken from maps-> map comparison) (is that a good workflow? what you guys do?) ...but some of the maps take a lot of time to compute. So any help will be appreciated. Thanks

4 3

AutoSol invalid MTZ column_types error
by Stan Yoo 20 Jan '17

20 Jan '17

Hello, I am getting an error message "Invalid MTZ column_types for the given miller_array." while I try to do AutoSol. The last line in the log is "Adding array ['N(+)', 'N(-)'] to output file with type II". Do you have any suggestion how to fix this error? Thanks

2 1

phaser.labin not respected
by Murpholino Peligro 20 Jan '17

20 Jan '17

When I do in the terminal: phenix.phaser phaser.hklin="out.mtz" phaser.labin="F(+),SIGF(+),F(-),SIGF(-),merged" phaser.model="prot.pdb" phaser.mol_weight=14400 phaser.model_rmsd=0.3 my log file says it is using F and SIGF: LABIN F = F SIGF = SIGF Why it does not respect the labels provided? or..Am I doing something wrong. PS MR is successful Thanks

2 2

help with Histidine flip in phenix refinement
by Vikram Dalal 19 Jan '17

19 Jan '17

Hi all, I have 4 Mn (2 Mn in each chain) in my protein structure. One Mn has 1 cordination with water, 1 cordination with His and 4 cordination with Asp. I model build the His in coot. Even this His is in bond range with Mn. But, when i refine this model in phenix. This His again flip other side (N terminal which has to cordinate with Mn goes to other direction). I am facing this problem only with His of A chain only while N of His of B chain are towards Mn only. Is there any option in pehnix refinment where we can exclude a specific residue or atom in refinment??

3 2

Phenix.refine Restraints: replicating refmac external restaints
by Elliot Nelson 19 Jan '17

19 Jan '17

Hi All, Looking to generate restraints for phenix.refine that are similiar/equivalent to external restraints in REFMAC. From over viewing the documentation i feel the correct way to do this is to generate bond restraints, i.e: Equivalent of: exte dist first chain A resi 38 atom C alte A second chain A resi 38 atom C alte B value 0.0 sigma 0.02 type 1 would be : refinment.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain A and resid 38 and altloc A and name C atom_selection_2 = chain A and resid 38 and altloc B and name C symmetry_operation = None distance_ideal = 0.0 sigma = 0.02 slack = None } } If this is incorrect: Am i missing another way to create external restraint functionality in phenix, or am I making a more fundamental misunderstanding of how restraints are handled in both programs? Thanks in advance Elliot Nelson

2 2

QuantumBio Release: XModeScore & DivCon Discovery Suite v7.1
by Lance Westerhoff 17 Jan '17

17 Jan '17

Hello All- I trust everyone had a nice holiday break and a Happy New Year! Today, we are excited to kick the new year off with a new release of our QM/MM refinement and analysis plugin for the Phenix platform. The full announcement, along with links to the details and licensing information, is available at this URL: http://www.quantumbioinc.com/news/show/DDS-012017 Thanks to our many users - academic, industrial, and government - who have provided feedback and support for this effort. This plugin, available within the DivCon Discovery Suite version 7.1, has a number of significant improvements applicable to users of Phenix including: * QM/MM X-ray Refinement Standard: Version 7.1 represents a complete overhaul of our MM and QM/MM implementation for improved stability, performance, and usability. Our fully automated QM/MM implementation has now come out of "beta" status and it is ready for production use. The implementation also supports truncated residues, multiple regions, and integrated ligand atom typing. * Application: Fragment Based Drug Design: Phenix/DivCon coupled with the novel, our patent pending XModeScore tool has been applied to several key areas including protomer/tautomer determination, binding mode selection, crystal water positioning, and now even fragment-based screening. We have provided a tutorial of MOE-based fragment docking coupled with XModeScore-based selection. * New Structure/Chemistry Analyses: The question we often hear from new users is how one can evaluate the performance of QM and QM/MM X-ray refinement vs. more conventional methods. We have now packaged several before/after analyses within refinement including Clash Scores (using phenix.molprobity); Strain, Interaction Energies, and ZDD (using DivCon); and GBVI/WSA dG binding score prediction (using MOE - as available). * New Feature [beta] - Protonation: Fast, integrated protonation and hydrogen bond network optimization is a perpetual problem in the field (especially in X-ray crystallography). This method uses a combination of dead end elimination and graph theory along with crystallographic symmetry and density - as available - to quickly and accurately determine the correct protonation states of bound ligands, active sites, waters, and protein/DNA/RNA. If you are interested in using or evaluating our linear scaling, quantum mechanics software in your drug discovery efforts or if you would like to schedule an on-line or on-site meeting to discuss the technology, please email sales(a)quantumbioinc.com and let us know. And as with last year, we are waiving the license free for non-profit, academic users as per academic license agreement. Our academic, commercial, consulting, and evaluation licenses are available on-line (most for electronic signature): http://www.quantumbioinc.com/products/software_licensing Have a great 2017! -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909 This message and any attachments are solely for the intended recipient and should be considered confidential. If you are not the intended recipient, please immediately and permanently delete.

1 0

Berkeley Server Downtime (1/13 - 1/14)
by Billy Poon 16 Jan '17

16 Jan '17

Dear all, On Friday, January 13, our servers will be shut down starting at 5:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available the next day (1/14) by 6:00 pm Pacific at the latest. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

1 3

Calculation of bond lengths, angles and torsion angle for large number of proteins
by Ashraya Ravikumar 12 Jan '17

12 Jan '17

Hi All, I would like to calculate all the bond lengths, bond angles and main chain torsion angles for a large set of proteins, in PDB format. Could you please let me know which module/command in phenix is suitable for this task? Regards, Ashraya

2 3

Re: [phenixbb] Modified DNA residue
by Pavel Afonine 12 Jan '17

12 Jan '17

Hi Melissa, we need to have a closer look to understand what's happening... Could you please send us these PDB file: - original (before modifications); - file after modifications; - file after refinement; - cif file. Pavel On 1/11/17 14:15, Melissa Ford wrote: > I'm having working on modeling a sulfur on the phosphate backbone of > DNA in replace of one of the oxygens and have encountered some > restraint problems. I've successfully managed to replace the oxygen > with a sulfur in the proper geometry in a pdb, generate a cif file for > the modified residue (adenosine 5'-phosphorothioate), and run an > initial refinement. Upon that refinement, a few errors occur. First, > since the phosphate bound to the sulfur is the first atom of the > modified residue the angle between the O3' (of the neighboring > residue) - P- S is not recognized and forced into an unfavorable > geometry. When trying to add that additional angle to the cif file, I > get an error. Aditionally, the change causes Phenix to not recognize > the chirality of the C3' that the phosphate is bonded to and forces > the ribose into a planar conformation. I am sure there is something I > am missing that allows phenix to recognize this new residue as a > modified nucleotide so that it knows these restraints. Any insight on > this would be great. Thank you!

1 0

Modified DNA residue
by Melissa Ford 12 Jan '17

12 Jan '17

I'm having working on modeling a sulfur on the phosphate backbone of DNA in replace of one of the oxygens and have encountered some restraint problems. I've successfully managed to replace the oxygen with a sulfur in the proper geometry in a pdb, generate a cif file for the modified residue (adenosine 5'-phosphorothioate), and run an initial refinement. Upon that refinement, a few errors occur. First, since the phosphate bound to the sulfur is the first atom of the modified residue the angle between the O3' (of the neighboring residue) - P- S is not recognized and forced into an unfavorable geometry. When trying to add that additional angle to the cif file, I get an error. Aditionally, the change causes Phenix to not recognize the chirality of the C3' that the phosphate is bonded to and forces the ribose into a planar conformation. I am sure there is something I am missing that allows phenix to recognize this new residue as a modified nucleotide so that it knows these restraints. Any insight on this would be great. Thank you!

1 0

error message after running phenix.refine: Unable to create Kinemagefile: float division by zero
by Georg Mlynek 11 Jan '17

11 Jan '17

Dear All, I getting this error message at the end of running phenix.refine: Unable to create Kinemagefile: float division by zero I just get this running phenix.refine on a neutron structure. Joint refinements are fine. I am using dev-2621 and ubuntu 15.10. Thanks in advance best regards, Georg.

2 1

8th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 11 Jan '17

11 Jan '17

First announcement 8th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 5 - June 9, 2017 Detailed information can be found on the workshop web page: https://conference.sns.gov/event/66/ Application deadline: April 22, 2017 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. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome - however the course organization is not able to support travel or accommodation. The number of participants will be limited to 15. There is no registration fee for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 22, 2017. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

1 0

Scientist position at AbbVie
by Longenecker, Kenton L 10 Jan '17

10 Jan '17

Hi - Please see the following job opportunity below and find full description to apply at: http://abbvie.taleo.net/careersection/jobdetail.ftl?job=1608252&lang=en Senior Scientist II, Structural Biology-1608252 AbbVie (NYSE:ABBV) is a global, research-based biopharmaceutical company formed in 2013 following separation from Abbott Laboratories. The company's mission is to use its expertise, dedicated people and unique approach to innovation to develop and market advanced therapies that address some of the world's most complex and serious diseases. AbbVie employs approximately 28,000 people worldwide and markets medicines in more than 170 countries. Description The Protein Crystallography Group at AbbVie Headquarters in Lake County, Illinois is seeking a highly motivated scientist to join our Structure-Based Drug Discovery team. The ideal candidate should have extensive hands-on experience in modern X-ray Crystallography techniques and computational methods of molecular structure analysis. As part of multidisciplinary teams, the Senior Scientist will utilize fragment-based strategies to identify ligands and provide insight to advance drug discovery targets through structure-based design. The successful candidate will contribute to drug discovery projects across the portfolio of AbbVie interests that also include therapeutic antibodies and novel biologics. ________________________________ Kenton Longenecker, Ph.D. Principal Scientist AbbVie R&D Discovery, DCAT Structural Biology 1 N. Waukegan Road, AP10-LL North Chicago, IL 60064 OFFICE 847-938-1428 EMAIL kenton.longenecker(a)abbvie.com<mailto:%[email protected]> abbvie.com<http://www.abbvie.com> This communication may contain information that is proprietary, confidential, or exempt from disclosure. If you are not the intended recipient, please note that any other dissemination, distribution, use or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or by return e-mail and delete it from his or her computer. ________________________________

1 0

Academic position in glycoscience at The University of York
by Jon Agirre 09 Jan '17

09 Jan '17

Not to be confused with our previous job posting - please note the earlier deadline (5th of February) for this one! The Department of Chemistry at The University of York is seeking to appoint a high-calibre researcher in glycoscience with a clear vision to lead their own programme of excellent research, which will complement that of Professor Gideon Davies, FRS FMedSci and other members of the York Structural Biology Laboratory (YSBL). The role is available at any level and we welcome interest from talented academics with an impressive research profile appropriate to the level of application and a collegiate approach to their work. We would particularly welcome applications from researchers with a track record in chemical biology approaches to mammalian glycoscience; preferably with biomedical aspects. You will join a department renowned internationally for its research. Combined with a dedication to high-quality teaching and excellent student satisfaction, we are recognised consistently for our family-friendly policies and are proud of our Athena SWAN Gold Award. Key Requirements (viewed relative to the level of post applied for – see candidate briefs for more details): - PhD in a Chemical or Biochemical Science - Demonstrated expertise in a field/fields central to glycoscience - Ability to undertake high-quality research and publish in leading, peer-reviewed journals - Ability to define, lead, manage and attract funds for research, operating across disciplinary boundaries - Experience of and commitment to teaching and learning at undergraduate level. - Demonstrable capacity for creative thinking and planning - Substantial recent publication record in leading peer-reviewed journal - Evidence of national and/or international collaboration More information: https://jobs.york.ac.uk/wd/plsql/wd_portal.show _job?p_web_site_id=3885&p_web_page_id=297414 Deadline for applications: 05/02/2017 -- Dr Jon Agirre York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, England http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ +44 (0) 1904 32 8270

1 0

Academic position in cryoEM at The University of York
by Jon Agirre 09 Jan '17

09 Jan '17

The Department of Chemistry at The University of York is seeking to appoint a high-calibre researcher in cryo-electron microscopy, with a clear vision to lead their own programme of excellent research within the York Structural Biology Laboratory (YSBL). Your research will complement the X-ray crystallography and NMR techniques currently used in the YSBL, and will bridge the gap between X-ray work and the optical microscopy in the Biology Technology Facility. The role is available at any level and we welcome interest from talented academics with an impressive research profile appropriate to the level of application and a collegiate approach to their work. You will be a dynamic research leader with a consistent track record in the application of cryo-electron microscopy to challenging biochemical/biological problems. We welcome applications from researchers with an interest in diverse areas of structural and cell biology, with particular interest in those working on mammalian systems. You'll join a department renowned internationally for its research. Combined with a dedication to high-quality teaching and excellent student satisfaction, we are recognised consistently for our family-friendly policies and are proud of our Athena SWAN Gold Award. Key requirements: (viewed relative to the level of post applied for – see candidate briefs for more details): - PhD in Chemical, Biochemical or Physical Sciences - Specialist knowledge in cryo-electron microscopy - Ability to undertake high-quality research and publish in leading, peer-reviewed journals - Ability to undertake high-quality research and publish in leading, peer-reviewed journals - Ability to define, lead, manage and attract funds for research, operating across disciplinary boundaries - Experience of and commitment to teaching and learning at undergraduate level. - Demonstrable capacity for creative thinking and planning - Substantial recent publication record in leading peer-reviewed journals - Evidence of national and/or international collaboration More information: https://jobs.york.ac.uk/wd/plsql/wd_portal.show _job?p_web_site_id=3885&p_web_page_id=297412 Deadline for applications: 12/02/2017 -- Dr Jon Agirre York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, England http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ +44 (0) 1904 32 8270

1 0

Multiple positions in Buffalo NY
by Edward Snell 06 Jan '17

06 Jan '17

Dear All, Just a reminder for those that may have missed it over the holidays. We have multiple positions for structural biologists in Buffalo NY. Please let anyone who may have an interest know of these opportunities. The first is with the Hauptman-Woodward Medical Research Institute: The Hauptman-Woodward Medical Research Institute (hwi.buffalo.edu) operates the High-Throughput Crystallization Screening Center providing crystallization and characterization services to the community at very competitive cost (www.getacrystal.org). A Ph.D. level research scientist position (post-doctoral or junior researcher) is available within the Center to guide operations on a daily basis, move research capabilities into production, and to help set the direction of the Center for the future. There is strong potential for both scientific growth and growth of responsibility. The candidate would be expected to have demonstrated expertise and productive research in the area along with appropriate publications. In addition to crystallization knowledge, experience with structural biology techniques in general is desired. Computational experience is a plus. The candidate should gave excellent communication, reading, writing, and presentation skills. They should be able to be a representative of the Center in the scientific community. They should have a good interpersonal skill set and be able to work with a diverse group. Evidence of seeking their own research funding would be viewed as a strong positive and the position would encourage the development of capabilities through active research efforts and collaboration. The Center interacts with both academia and industry and provides some crystallization screening services for a growing Gene to Structure company, HarkerBIO, (www. harkerbio.com). Collaborative possibilities are possible in this area. Research facilities at the Center include liquid handling robots, in-house developed plate imaging capabilities, SONICC and UV analysis, and X-ray analysis. The Center is well connected to several synchrotron facilities. A sophisticated computational infrastructure is in place. In both the X-ray and computational side, research advances are ready to be implemented into the Centers capabilities. The Hauptman-Woodward Medical Research Institute is 60 years old and based in Buffalo New York. It is at the center of a rapidly expanding medical campus. Good benefits are provided and the cost of living in the area is very competitive. For those with a focused research interest, the Institute is located adjacent to high-end computer facilities, a Comprehensive Cancer Center, a new Medical School under construction, and multiple biotech startup companies. Collaborative efforts with academic and industrial collaborators are strongly encouraged and aided by an umbrella organization on the campus. The Hauptman-Woodward Medical Research Institute, Inc. as an equal opportunity employer, extends employment opportunities to qualified applicants and employees on a non-discriminatory basis without regard to race, color, sex, creed, age, religion, national origin, marital status, veteran status, sexual orientation, genetic predisposition, carrier status, or disability that would prevent the performance of the essential requirements of the job with or without a reasonable accommodation in compliance with the appropriate New York State and Federal laws, or any other legally protected characteristics. This policy applies to all conditions and terms of employment. Formal applications should send a cover letter and resume along with three contacts for references to opportunity(a)hwi.buffalo.edu. The position is available in the New Year and will be open until filled. And on behalf of Artem Evdokimov, HarkerBIO CEO, the other positions are with a company called HarkerBIO housed in the Hauptman-Woodward Medical Research Institute building: HarkerBIO is hiring two *Research Scientist - Structural Biology * positions. Desired qualifications are quite broad, but can be summarized as follows: 1) someone who is a start-up enthusiast, not afraid of a challenge and has both the desire to innovate in science and the ability to do so. A PhD in related area is a plus, however we would consider qualified M.Sc. candidates. 2) someone with a relevant experience in at least 70% of the gene to structure 'process' - in other terms, the candidate is able to perform literature research, design clones, clone, express, purify, crystallize and solve structures -- or at least a good chunk of the above. Ideally someone with experience in mammalian and/or insect cell expression, and/or membrane protein work. 3) a scientist with a reasonably rounded skill set in biophysical characterization of macromolecules (SPR, DSF, anSEC/MALS, and so forth) 4) deep interest in developing structure-related technologies (e.g. expression systems, crystallization research, etc.). Desire and ability to participate in internal research projects. 5) high work ethic, impeccable documentation abilities, sense of humor 6) committed to relocating to Buffalo, NY HarkerBIO offer: Competitive salary (commensurate with experience) and full benefits Energetic and friendly work environment Coverage of reasonable relocation expenses for highly qualified candidates Co-location with a nonprofit research institute (HWI) and participation in the thriving research community at the Buffalo-Niagara Medical Campus HarkerBIO is an EO/AA employer. Please direct your inquiries to careers(a)harkerbio.com<mailto:[email protected]>. Note that for both positions, applications should be addressed to the emails given in the position descriptions. Happy New Year, Eddie Edward Snell Ph.D. President and CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, University at Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 hwi.buffalo.edu Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu [cid:[email protected]] Heisenberg was probably here!

1 0

Phenix.model_vs_data - Rfree difference
by Luca Pellegrini 03 Jan '17

03 Jan '17

Hello, I am trying to find out the reason for a large R-free difference that I am getting between phenix.refine and phenix.model_vs_data: phenix.refine R-work/R-free 0.1702/0.1974 phenix.model_vs_data R-work/R-free 0.1728/0.1795 Initial refinement was using the intensities in an XDS_ASCII.HKL dataset, followed by a few refinement cycles against the same dataset, but using amplitudes calculated in Aimless, with the ‘skip scaling just merge’ option and keeping the FreeR reflections. When I checked R-free values for the last refinement run before the conversion, there was no large discrepancy: phenix.refine R-work/R-free 0.1720/0.2086 phenix.model_vs_data R-work/R-free 0.1715/0.2080 Can anyone please advise? Apart from this, refinement went well - both the 1.9A map and the model look fine. Thanks for the help & happy New Year, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469

2 1

Postdoctoral Fellow Position at US MHRP, WRAIR
by gjoyce＠hivresearch.org 30 Dec '16

30 Dec '16

Dear All, A postdoc position is available in a newly formed Structural Biology Section, part of the US Military HIV Research Program, WRAIR in Silver Spring, Maryland, USA. The position involves the application of structural biology to understanding viral glycoproteins and the immune response following vaccination or natural infection. Interested and qualified individuals can apply through the following official link at Job ID: 212324 at the Henry M Jackson Foundation careers website: http://www.hjf.org/careers/open-jobs. Applicants must be US citizens or have lived in the US for at least 3 consecutive years. Please feel free to contact me at gjoyce(a)hivresearch.org if you have any questions. Best wishes, Gordon HJF is seeking a Postdoctoral Fellow to support the Military HIV Research Program (MHRP) located at the Walter Reed Army Institute of Research (WRAIR) in Silver Spring, Maryland. The incumbent will be responsible for initiating and carrying out scientific projects, under the supervision of senior scientists and in collaboration with other research scientists. The position involves the characterization of the humoral immune response to HIV-1 infection and HIV-1 vaccines using X-ray crystallography. The incumbent will be responsible for conducting and publishing research in HIV structural biology. The incumbent will work within a multidisciplinary environment consisting of military, government, academic, and international collaborators. Responsibilities: Conducts independent research and learns techniques required to conduct the research. Assists in designing, developing, executing, and implementing scientific research and/or products. Develops a thorough understanding of the scientific literature relating to the research topics. Collects and handles samples and keeps detailed inventory and records of experiments by maintaining up to date, clear, and accurate laboratory notebooks. Executes projects related to biochemical and structural characterization of antibodies, vaccine candidates and their complexes. Analyzes experimental data, applying relevant statistical and bioinformatic models. Presents data at scientific meetings and publishes original research in peer-reviewed journals. Assists with training laboratory staff and collaborates with labs within and outside of MHRP. Follows all MHRP and WRAIR safety procedures and completes required training in a timely manner. Performs other duties as assigned. Required Knowledge, Skills, and Abilities: PhD in structural biology or related area with significant experience in X-ray protein crystallography. Knowledge of appropriate scientific area; ability to analyze and interpret data. Experience and proficiency in protein purification, protein characterization, X-ray crystallography including up-to-date knowledge of relevant programs including CCP4, and Phenix packages. Experience with project planning, implementation, and data analysis. Experience in presenting at scientific meetings and writing manuscripts for scientific journals. Practical knowledge of electron microscopy, molecular modelling or structure-based mutagenesis and design is an advantage. Minimum Education/Training Requirements: Ph.D. in structural biology, molecular biology, immunology, microbiology, biochemistry or related discipline. Minimum Experience: 0-2 years of postdoctoral experience Physical Capabilities: Long periods of standing and sitting; intricate work with hands; carrying of light and moderately heavy laboratory equipment. Job performance requires movement around and between several laboratories, and long periods of sitting at laboratory bench. Fine motor coordination in manipulation of laboratory materials is essential. Supervisory Responsibilities/Controls: May provide guidance to laboratory staff. Work Environment: Laboratory environment; may require working evenings and weekends. The incumbent will be expected to practice safe handling of hazardous chemicals. This laboratory is densely populated and requires good interpersonal skills for effective job performance. This position requires working and occasional travel to US synchrotron facilities. This Postdoctoral Fellow will support the US Military HIV Research Program, located at The Walter Reed Army Institute of Research (WRAIR) in Silver Spring, MD. HJF is an equal opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, or protected veteran status. Any qualifications to be considered as equivalents, in lieu of stated minimums, require the prior approval of the Director of Human Resources. M. Gordon Joyce, Ph.D. Chief, Structural Biology Section The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF) US Military HIV Research Program (MHRP) Walter Reed Army Institute of Research (WRAIR) 1N33, 503 Robert Grant Ave, Silver Spring, MD 20910 Office: 301-319-7528 Cell: 240-672-4311 gjoyce(a)hivresearch.org Web: www.hivresearch.org Facebook: www.facebook.com/hivresearch YouTube: www.youtube.com/mhrpvideos Twitter: www.twitter.com/mhrpinfo The U.S. Military HIV Research Program (MHRP), centered at the Walter Reed Army Institute of Research (WRAIR), is an international HIV vaccine research program that successfully integrates HIV/AIDS prevention, care and treatment.

1 0

Spring 2016 MicroED workshops at Janelia Research Campus
by Hattne, Johan 23 Dec '16

23 Dec '16

Due to high demand, two back-to-back MicroED workshops will be held at Janelia Research Campus (Ashburn, VA) in the spring. The workshops are hosted by Tamir Gonen and will have the same content. Accepted participants will be assigned by the organizers to one or the other (not both). May 21-24 and May 24-27, 2017 MicroED is a cryoEM method that uses electron diffraction to facilitate structure determination from sub-micron sized 3D crystals, eliminating the need to grow large crystals. MicroED uses equipment and procedures that are standard on many cryoTEM:s, and because of this the technique can be easily adopted in labs and facilities around the world. To facilitate the widespread use of MicroED, we are offering these workshops to teach microscopists how to perform the technique and adopt it at their own institutions. There is no registration fee for participation, and Janelia will provide on-site housing and meals. Attendees are expected to cover their own travel expenses and must be able to stay for the duration. Applicants must register and submit a brief statement on why they wish to participate, via our online registration system. https://conference.janelia.org Please note that this system is designed to collect abstract information for presentations. Please write your statement of interest in the "abstract" field, put your name in the "author" field, and put "n/a" in the "presentation title" and "keyword" fields. Space in these workshops is limited. The application deadline is February 10, 2017. // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

1 0

Job opportunity - Structural Biology GSK Vaccines
by Enrico Malito 22 Dec '16

22 Dec '16

Dear phenix community, The Structural Biology Lab at GSK Vaccines, Rockville, MD, USA, is seeking a candidate for a Scientist/Senior Scientist position (Job ID: 148543, hiring managers: Enrico Malito, Matthew Bottomley). We offer outstanding opportunities and compensation to outstanding candidates. Anyone interested to apply can do so by visiting this link: https://careers.peopleclick. com/careerscp/client_gsk/external1931/en-us/gateway.do? functionName=viewFromLink&jobPostId=323652&localeCode=en-us (Please note that this may wrap to another line of text; you may need to copy and paste the entire URL into your browser window). Applications will be accepted only through the page at the link above. Examples of relevant recent publications: - Rappuoli et al 2016. Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design. http://dx.doi.org/10.1084/jem.20151960 - Chandramouli et al 2015. Structure of HCMV glycoprotein B in the postfusion conformation bound to a neutralizing human antibody http://dx.doi.org/10.1038/ncomms9176 - Ciferri et al 2015. Antigenic Characterization of the HCMV gH/gL/gO and Pentamer Cell Entry Complexes Reveals Binding Sites for Potently Neutralizing Human Antibodies http://dx.doi.org/10.1371/journal.ppat.1005230 - Malito et al 2015. Protein Crystallography in Vaccine Research and Development. http://dx.doi.org/10.3390/ijms160613106 Yours sincerely, *Enrico Malito, PhD* *Lab Head of Structural Biology and BiophysicsGSK VaccinesPreclinical R&D USGSK Vaccines14200 Shady Grove Road, Rockville MD 20850, USA*

1 0

alingments in mr_rosetta
by Kajander, Tommi A 21 Dec '16

21 Dec '16

Hi, I am wondering about the alignment of sequence and PDB model in mr_rosetta - the program seems to complain if the sequences dont exactyl match - so is this really the case? (I have an initial model from autobuild with some fragments that do not have fully correct sequence - hence it doenst exactly match with the original sequence of the protein). Does it have to? Or should there be a way around it? also the command file examples online e.g. : phenix.mr_rosetta \ seq_file=seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ already_placed=True \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies=2 \ space_group=p212121 \ use_all_plausible_sg=False \ nproc=200 \ group_run_command=qsub when using the command file all the commands are not recognized for some reason (running on a mac with bash shell) e.g. rescore_mr.relax=False, same with fragment files… not quite sure what the problems is there, probably something trivial. -if i just enter them on the command line it works. Thanks, Tommi

2 1

Error from f_model_all_scales.py
by John Bruning 20 Dec '16

20 Dec '16

Hi (Pavel), I have a dataset (P31) which I am processing with the pairwise combinations of reindexing operators (4 incl. no reindexing therefore h,k,l) and twin laws (4 incl. no twinning as h,k,l). While some of these combinations are fine during refinement (Vers 1.11.1), for some combinations I get the following error, which ultimately kills the refinement. Thanks in advance and apologies if I am missing something stupid. Incidentally, a different dataset seems to tolerate all combinations. *approx_equal eps: 1e-05* *approx_equal multiplier: 10000000000.0* *0.512707954357 approx_equal ERROR* *0.514972857238 approx_equal ERROR* Traceback (most recent call last): File "/Applications/phenix-1.11.1-2575/build/../modules/phenix/ phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/command_line.py", line 154, in run call_back_handler=call_back_handler) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/driver.py", line 1529, in run call_back_handler = call_back_handler).result File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/strategies.py", line 121, in __init__ log = log) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/fmodels.py", line 159, in run fmodel.update_solvent_and_scale(initialise=True) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/twinning/twin_f_model.py", line 797, in update_solvent_and_scale params=params, log=log, apply_back_trace=apply_back_trace) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1457, in update_all_scales params = params, log = log, refine_hd_scattering=refine_hd_scattering) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 38, in __init__ refine_hd_scattering = refine_hd_scattering, log = log) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 61, in compute refine_hd_scattering = refine_hd_scattering) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 329, in update_solvent_and_scale_twin * assert approx_equal(self.r_all(), o_kbu_sol.r(), 1.e-5)* *AssertionError*

1 0

phenix rosetta interface
by CPMAS Chen 17 Dec '16

17 Dec '16

Hi, All, When I compile phenix-1.11-2567 and rosetta-bin-mac_2016.37.58930_bundle interface, I got the following error message. Any suggestion to fix this? Thanks! src/core/scoring/cryst/PhenixInterface.cc:253:11: error: no matching member function for call to 'dump_pdb' pose_asu.dump_pdb( pdbout , "1" ); ~~~~~~~~~^~~~~~~~ src/core/pose/Pose.hh:1525:2: note: candidate function not viable: no known conversion from 'char [256]' to 'std::ostream &' (aka 'basic_ostream<char> &') for 1st argument dump_pdb( ^ src/core/pose/Pose.hh:1518:2: note: candidate function not viable: requires single argument 'file_name', but 2 arguments were provided dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate function not viable: requires single argument 'out', but 2 arguments were provided dump_pdb(std::ostream & out) const; ^ src/core/scoring/cryst/PhenixInterface.cc:916:11: error: no matching member function for call to 'dump_pdb' pose_asu.dump_pdb( buffer , "1" ); ~~~~~~~~~^~~~~~~~ src/core/pose/Pose.hh:1525:2: note: candidate function not viable: no known conversion from 'char [256]' to 'std::ostream &' (aka 'basic_ostream<char> &') for 1st argument dump_pdb( ^ src/core/pose/Pose.hh:1518:2: note: candidate function not viable: requires single argument 'file_name', but 2 arguments were provided dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate function not viable: requires single argument 'out', but 2 arguments were provided dump_pdb(std::ostream & out) const; ^ 2 errors generated. scons: *** [build/src/release/macos/16.1/64/x86/clang/8.0/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: building terminated because of errors. Thanks! -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

1 0

Asymmetric unit content
by Sharan Karade 13 Dec '16

13 Dec '16

Dear all, I have solved the structure in C121 space group, having five molecules in asymmetric unit, my supervisor have doubt about the fifth molecule becoz of poor density fit, if i delete the fifth molecule, there is a space for the molecule and crystal is not continuous, i calculated difference map from Phenix by deleting fifth molecule and got the Map showing presence of molecule. My supervisor want me to get SetMet data, but crystals are diffracting poor (7A). Is there any way to convince my guide. advance thanks for valuable suggestions. -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

5 8

Recent improvements in Phaser for systematically weak data
by Randy Read 09 Dec '16

09 Dec '16

Dear all, Between the last official release of Phenix (version 1.11.1-2575, released on 26 October) and a recent CCP4 update (7.0.023 released on 23 November), we fixed a problem in which the fast rotation function was not properly accounting for the effect of measurement errors in intensities. Under many circumstances (i.e. with well-measured data to the resolution needed to solve the structure by MR), the change is not noticeable. However, if you have systematically weak data (particularly from high levels of anisotropy or potentially from the effects of translational non-crystallographic symmetry), the fix can mean the difference between failing to solve the structure, because the correct orientation has not been generated, or solving it with a default run of Phaser. We recommend that anyone trying to solve a structure with substantial anisotropy (anisotropic deltaB of 50 A^2 or greater) and/or translational NCS should update to a newer version of either package. If you're using CCP4, you should get the latest update, because there was a problem with the version of coot distributed with the 7.0.023 update. If you're using Phenix, you should get a recent nightly build, i.e. dev-2608 or something even newer. Please note that you want to provide data to Phaser in the form of intensities rather than amplitudes to get the best results for such data! So far, I've found 3 of our test cases where this makes a real difference, but I would be interested in hearing from anyone who finds that this makes a difference for other cases. Best wishes, Randy Read ------ 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

1 0

iNEXT access: NMR Extended Support and more!
by Anastassis Perrakis 06 Dec '16

06 Dec '16

Dear all, I should perhaps offer sincere apologies for posting the crystallography boards with NMR news ;-). However, I will not do that, as I sincerely hope you will see that in an era of integration of structural methods, such opportunities can offer the chance for excellent and exciting scientific endeavours. iNEXT (http://www.inext-eu.org <http://www.inext-eu.org/>) is committed to bring structural methods closer to non-experts, by funding access to world class infrastructures for Structural Biology. Major tools for achieving that goal are the so-called Extended Support modalities. We are happy to announce the start for acess to the iNEXT Enhanced Support modality for NMR (NMR assignment, structure, dynamics). In this mode, the NMR groups in Florence, Frankfurt and Utrecht are involved in guiding and training NMR novices. This iNEXT access modality also targets "new users with backgrounds other than Structural Biology”, so please feel free to forward that also to your biochemistry friends. Facility personnel will be involved to guide assignments, titrations, structure calculations, relaxation analyses, etc. I also want to bring your attention to a few more iNEXT news: - The Structural Audit, now allows multiple samples in a related project to be submitted in a single application for stability assessment and crystallisation screening; a basic analysis by SAXS, EM, or NMR is also supported (single click in application!) if an appropriate sample is available. - The Enhanced Support modality "From macromolecular sample to X-ray data collection” is now better integrated with Structural Audit; applications can be combined, so in case of a successful Audit, you could rapidly proceed to further X-ray experiments (crystal optimisation, SAXS and/or crystallography) - The Enhanced Support modality "Advanced light imaging” to support structural studies with in cells measurement of protein interaction kinetics, have also been made recently available. - The Enhanced Support modality "Cryo-EM sample optimisation” for hands-on assistance in optimizing a sample for single particle EM is a great chance to move your sample towards cryo-EM! - The Enhanced Support modality "Macromolecular interactions” is your chance for access to a Biophysics facility with various instruments and hands-on support for performing and analysing experiments to quantify a variety of interactions. - All the High-End modalities (X-rays, NMR, cryo-EM) are always open for access! So, please, submit your proposal now! <https://www.structuralbiology.eu/update/submit-proposal?t=inext> … and keep in mind that a limited amount of the funding (~10%) can go towards projects that are not in an EU-country or associated country. On behalf of the iNEXT Management, Best wishes, Tassos Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

1 0

phenix.real_space_refine crashes for very large pdb files
by #AHMED TOFAYEL# 02 Dec '16

02 Dec '16

Dear developers and users, My phenix.real_space_refine run crashes with the error mentioned below when I have used following command to run it on a complete ribosome (containing coordinates for small subunit and large subunit in a single pdb file): phenix.real_space_refine model.pdb map.mrc resolution=4.5 reference_coordinate_restraints.enabled=true reference_coordinate_restraints.selection="chain A and resseq 2:700" reference_coordinate_restraints.sigma=0.05 secondary_structure.enabled=True res.eff > out.out >From the out.out file I can see that, it ran for 5 macro_cycles and started group b-factor refinement which reads (last few lines): |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.144348 restraints weight = 1067.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147257 restraints weight = 482.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149066 restraints weight = 262.900| |-----------------------------------------------------------------------------| The run crashes at this point.... However, phenix.real_space_refine runs fine when I am refining a protein chain or a complex (for eg: just the large or the small subunit of a ribosome). Does it have to do with my pdb file being so big after merging of both subunits where I have also crossed 99999 atoms and atom serial numbers start from A0000? A related question: What is the latest consensus of using chain IDs and atom serial numbers to use in phenix.real_space_refine for handling large files like ribosome pdbs ? I have found some information on: http://cci.lbl.gov/hybrid_36/ The error in terminal reads: Traceback (most recent call last): File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 782, in <module> o = run(sys.argv[1:]) File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 518, in __init__ self.caller(func = self.run_macro_cycles, prefix="Macro-cycles") File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 547, in caller status = func(prefix=prefix, **kwargs) File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 540, in run_macro_cycles log = self.log) File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 66, in __init__ self.caller(self.refine_adp, "ADP refinement") File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 71, in caller status = func(prefix=prefix) File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 317, in refine_adp adp_refinery.refine() File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/refinement/real_space/adp.py", line 78, in refine b_isos_refined = self.refine_box_with_selected(selection=sel) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/refinement/real_space/adp.py", line 56, in refine_box_with_selected fmodel.update_all_scales(update_f_part1=False, apply_back_trace=True) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1452, in update_all_scales self.apply_scale_k1_to_f_obs() File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1500, in apply_scale_k1_to_f_obs r_start = self.r_work() File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 2004, in r_work selection = selection) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1972, in _r_factor f_model = self.f_model_scaled_with_k1_w().data() File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1730, in f_model_scaled_with_k1_w data = self.scale_k1_w()*self.f_model_work().data()) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 2048, in scale_k1_w selection=selection) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 182, in _scale_helper raise RuntimeError("Zero denominator in scale calculation.") RuntimeError: Zero denominator in scale calculation. Best regards, Tofayel

2 2

difference map based on the cryo-EM map
by Smith Lee 02 Dec '16

02 Dec '16

Dear All, Supposed by phenix.real_space_refine I got a PDB of protein-ligand, will you please let me know how to get the subtraction map (difference map?) which only show the density of the ligand, so that I can see whether the ligand was well resolved in the map, or whether the built ligand fits well with the ligand density? Smith

2 1

Incrementing high resolution cutoff in phenix.mtz2map or phenix.cut_out_density
by Andrew Morin 01 Dec '16

01 Dec '16

Hello, I am trying to find a convenient way to generate maps using phenix.mtz2map at increasingly greater values of d_min. For example: I have a .mtz file of a structure solved at 2.4A. I run phenix.mtz2map with d_min=none and obtain a map using all of the resolution data. I would like to also create 10 more maps with d_min = 3.4, 4.4, 5.4, 6.4,...12.4A. An mtz of 1.7A would increment at 2.7, 3.7...11.7A, etc. Might anyone know of a handy way to automate this over a large number of mtz files? ALTERNATIVELY - I am performing a phenix.cut_out_density step prior to this. So if it might be easier to automate a incrementing high resolution cutoff in phenix.cut_out_density, that would also work. Thanks for your help. -Andrew

5 5

Refine only selective chains in a complex using phenix.real_space_refine
by #AHMED TOFAYEL# 30 Nov '16

30 Nov '16

Dear all, Is it possible using phenix.real_space_refine to locally refine a protein or RNA chain (against a cryo-EM map) which is part of a big complex. During the run, I would like to keep most of my complex constant in space except neighboring one or two protein/RNA molecules which I would like to see getting adjusted to remove clashes. I am using the program through command-line. Best regards, Tofayel NTU Singapore

2 2

Can't Run Rosetta_refine
by NISHANT SINGH 30 Nov '16

30 Nov '16

Hi Everyone, I am trying to run Phenix's rosetta refine. I seem to have downloaded and compiled the rosetta package fine, as I got the following statement after compiling was done: scons: done building targets. but I am failing at running: rosetta.build_phenix_interface. It says that command not found. I am attaching my env page with this email. bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$ env ROSETTA3_DB=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/database TERM_PROGRAM=Apple_Terminal SHELL=/bin/bash TERM=xterm-256color TMPDIR=/var/folders/cb/5v492std3d31jr42j7h3jm9h0000gp/T/ Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.KEC4L2Cjos/Render TERM_PROGRAM_VERSION=387 OLDPWD=/Applications TERM_SESSION_ID=A82EA51D-0920-4F3B-BE03-92AE0C40A44B USER=Kumar SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.tMihawGOC7/Listeners __CF_USER_TEXT_ENCODING=0x1F6:0x0:0x0 ROSETTA_BIN=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/source/bin PATH=/Library/Frameworks/Python.framework/Versions/3.5/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Users/Kumar/miniconda2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin PWD=/Applications/rosetta_bin_mac_2016.32.58837_bundle LANG=en_US.UTF-8 XPC_FLAGS=0x0 XPC_SERVICE_NAME=0 SHLVL=1 HOME=/Users/Kumar LOGNAME=Kumar DISPLAY=/private/tmp/com.apple.launchd.BhETYwyInl/org.macosforge.xquartz:0 PHENIX_ROSETTA_PATH=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH/ _=/usr/bin/env bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$ env ROSETTA3_DB=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/database TERM_PROGRAM=Apple_Terminal SHELL=/bin/bash TERM=xterm-256color TMPDIR=/var/folders/cb/5v492std3d31jr42j7h3jm9h0000gp/T/ Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.KEC4L2Cjos/Render TERM_PROGRAM_VERSION=387 OLDPWD=/Applications TERM_SESSION_ID=A82EA51D-0920-4F3B-BE03-92AE0C40A44B USER=Kumar SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.tMihawGOC7/Listeners __CF_USER_TEXT_ENCODING=0x1F6:0x0:0x0 ROSETTA_BIN=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/source/bin PATH=/Library/Frameworks/Python.framework/Versions/3.5/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Users/Kumar/miniconda2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin PWD=/Applications/rosetta_bin_mac_2016.32.58837_bundle LANG=en_US.UTF-8 XPC_FLAGS=0x0 XPC_SERVICE_NAME=0 SHLVL=1 HOME=/Users/Kumar LOGNAME=Kumar DISPLAY=/private/tmp/com.apple.launchd.BhETYwyInl/org.macosforge.xquartz:0 PHENIX_ROSETTA_PATH=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH/ _=/usr/bin/env bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$

2 1

kickmaps
by Veronica Fiorentino 26 Nov '16

26 Nov '16

Dear all, I am using the latest Phenix; Calculate Maps does not seem to have an option to for kickmaps as given in the https://www.phenix-online.org/documentation/reference/create_maps.html I have made a screenshot: http://imgur.com/a/upgqy Am I missing something obvious? Alternately, If anyone can share a script I would prefer it! many thanks Veronica

3 4

ensemble refinement crash.
by Rajendra Sharma 25 Nov '16

25 Nov '16

Dear all, I am running ensemble refinement using phenix-1.10. The calculations are running good until the Ensemble reducer where the jobs get killed in some cases automatically without giving output pdb. I am using default setting to run the jobs. pdb_stored_per_block is 50 totaling 500 towards the end. Is the crash happening because of memory? Will reducing the number of pdb per block help? Secondly, how can I restart the killed runs? thanks in advance. Raji *Rajendra SharmaResearch Scholar, PhD.* *Centro Nacional de Biotecnología <http://www.cnb.csic.es/>,* *Universidad Autónoma de Madrid,* *Madrid, Spain.Mobile No. +31-656688390*

2 2

Realspace refinement
by Reza Khayat 23 Nov '16

23 Nov '16

Hi, Does realspace refinement consider temperature factors during refinement? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070

6 15

Postdoctoral positions at the NIH in structural and mechanistic studies on integral membrane proteins
by Anirban Banerjee 19 Nov '16

19 Nov '16

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 biochemistry, electrophysiology together with synthetic chemistry 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 insect/mammalian expression systems 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.

1 0

Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 19 Nov '16

19 Nov '16

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission in the January 2017 issue is 15 December 2016. However, if you have a brilliant idea during your holiday break please don't hesitate to forward it. 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 33R0349, Molecular Biophysics and Integrated Bioimaging 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

gtk glib error messages and too large fonts when starting phenix 1.11.1-2575
by Martin Moche 19 Nov '16

19 Nov '16

Dear colleagues, Today I install latest stable phenix 1.11.1-2575 without problems - output attached. When starting the phenix GUI, the fonts are too large and I get a lot of Gtk, GLib error messages - see below These error messages can be found online as well https://mail.gnome.org/archives/meld-list/2015-January/msg00007.html and are therefore likely not related to phenix. Perhaps somebody knows how to get rid of them and get smaller fonts into phenix GUI? Best regards, Martin ############### my Glib Gtk error messages ############## [x_marmo@triolith2 ~]$ phenix (main.py:60858): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:60858): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:60858): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:60858): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:60858): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:60858): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:60858): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:60858): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed Already checked for new versions in last 24 hours, skipping Martin Moche, Ph.D. Head of Protein Crystallography Karolinska Institutet MBB/PSF Scheeles väg 2 171 77 Stockholm Sweden phone: +46-8-524 868 43 mobile: +46-73-322 93 27 fax: +46-8-524 868 68 email: Martin.Moche(a)ki.se

2 2

Sorry: Refinement of multiple models not implemented.
by Murpholino Peligro 17 Nov '16

17 Nov '16

I was looking at pdb 2d6b and I try to do a refinement with phenix. (First I generated the cif file with phenix.elbow for 202 ( https://www3.rcsb.org/ligand/202). Then I retry the refinement and I got the error "Sorry: Refinement of multiple models not implemented." How to proceed? Thanks MP

3 2