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Computational Crystallography Newsletter, Volume 8, Number 1
by Nigel Moriarty 06 Feb '17

06 Feb '17

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. January 2017 <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf> Articles - Deploying *cctbx.xfel* in Cloud Computing and High Performance Computing Environments <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=10> Short Communications - multi_core_run(), yet another simple tool for embarrassingly parallel jobs <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=6> - Phenix tool to compute a difference map for cryo-EM <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=8> Fitting tips #13 – O-pairs: The love-hate relationship of carboxyl oxygens <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=2> 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

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Scale and merge multiple data sets
by Sam Tang 05 Feb '17

05 Feb '17

Dear colleagues Hello again. I would like to scale and merge two different native datasets for a same protein complex (which semed to die off gradually in the beam) using the scale_and_merge tool. The error message was received "Multiple intensity arrays - please specify one: data_labels=I,SIGI data_labels=IPR,SIGPR" However I looked into the log file and I have actually included "data_labels = "IPR,SIGIPR,merged" . Perhaps I have missed something else in the setting? Regards Sam Sam Tang Biochemistry Programme, School of Life Sciences, CUHK

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protein atom selection
by wtempel 03 Feb '17

03 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

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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

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10th CCP4/APS Crystallographic School in the USA
by Sanishvili, Ruslan 01 Feb '17

01 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

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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

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Creating custom peptide bonds
by Pearce, N.M. (Nick) 31 Jan '17

31 Jan '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

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omit map problems
by Thomas, Leonard M. 31 Jan '17

31 Jan '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

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

30 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

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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

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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

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multi-domain protein data, and multi-component/full-featured Phaser-MR
by Emilia C. Arturo (Emily) 22 Jan '17

22 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

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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__'

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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

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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

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AutoSol invalid MTZ column_types error
by Stan Yoo 19 Jan '17

19 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

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phaser.labin not respected
by Murpholino Peligro 19 Jan '17

19 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

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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??

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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

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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.

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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

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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

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Re: [phenixbb] Modified DNA residue
by Pavel Afonine 11 Jan '17

11 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!

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Modified DNA residue
by Melissa Ford 11 Jan '17

11 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!

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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.

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