- phenixbb - phenix-online.org

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

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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

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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

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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) 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

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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 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

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