- phenixbb - phenix-online.org

phenix.model_vs_data enhancement request
by Schubert, Carsten [PRDUS] 18 May '11

18 May '11

Hi Pavel, do you think it would be possible to extend the statistics printed out by phenix.model_vs_data, so it also does a break-down by chains? Right now the stats are listed by residue type, i.e. protein/ligand/solvent/etc. For instance if I am interested in the B-factors of a glycosylated protein with ligands, the sugars and ligands all get muddled together. Breaking this down by chains as well would allow for finer control. Cheers, Carsten

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Polygon graphs
by Tanner, John J. 17 May '11

17 May '11

Does anyone know whether the polygon graphs from the following paper were ever incorporated into phenix? Crystallographic model quality at a glance Acta Crystallogr D Biol Crystallogr. 2009 March 1; 65(Pt 3): 297300. -- John J. Tanner Professor of Chemistry and Biochemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tannerjj(a)missouri.edu http://www.chem.missouri.edu/TannerGroup/tanner.html

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Phenix Refine
by Thomas C. Terwilliger 16 May '11

16 May '11

Hi Haytham, This means that you have two atoms in your pdb file that both have the name BR PDB F 1 You can find these with: grep 'BR' my_pdb_file.pdb |grep BR Let me know if that doesn't do it! All the best, Tom T >> when i refine using phenix.refine i get this error >> >> number of groups of duplicate atom labels:1 >> total number of affected atoms: 2 >> group "HETATM 3466 BR PDB F 1 .*. BR " "HETATM 3467 BR PDB F 1 .*. BR " >> >> could you please tell me what is that >> >> Haytham Wahba >> PhD stu >> UdeM >> >>

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Postdoctoral positions in structural biology
by Protein Crystallography 15 May '11

15 May '11

Postdoctoral positions are available immediately in the *Structural Biology Laboratory* headed by *Dr. C. S. Raman* at the University of Maryland, Baltimore. Research in the Raman laboratory combines structural, biophysical, biochemical, and cell biological approaches to understand the molecular mechanisms underlying cellular signaling. The laboratory is equipped with state-of-the-art equipment for fermentation, high-throughput protein expression, purification, crystallization (liquid handlers for screen generation and optimization, Mosquito LCP robot, and crystal imaging systems), X-ray diffraction, and high definition mass spectrometry (Synapt G2 HDMS). In addition, we have ready access to synchrotron facilities. For a representative example of our work, please consult*:* *Nature 455: 363-368*. Applicants should hold a PhD in biochemistry, biophysics, chemistry, molecular biology, or a closely related field. Applicants should have experience in protein crystallography as well as a good publication record. Strong background in protein expression and biophysical characterization is essential. Expertise in membrane protein purification is a plus. Furthermore, strong communication skills in oral and written English are required. To apply, please, send a letter of interest, a CV, and names of three references by e-mail to: craman(a)rx.umaryland.edu

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missing/extra atoms in phenix.refine
by R.M. Garavito 13 May '11

13 May '11

We are trying to finish up the refinement on two structures, but we have run into a strange problem that I have never seen before. So we need to ask the Phenix experts. As background, we recently solved the structure of an 808 residue enzyme, which crystallizes as a tetramer. In the asymmetric unit there are two tetramers (>6400 residues, ~52,000 atoms, but 67% solvent). After SAD phasing and autobuild (many kudos to the Phenix team), we were able to trace easily the chain in two different ligand complexes, one at 2.85 Å and the other at 2.8 Å. Although the C-terminal domains are quite well resolved (and obey 222 NCS), the first domain (~110 residues out of 808) is a bit disordered and shows some conformational differences between each monomer. While the main chain in this domain can be traced, side chain densities are mediocre to missing in spots. In order to ensure a consistent tracing and sequence assignment between all 8 N-terminal domain, we built in the "correct" sequence, but truncated the side chains to CB if the side chain density was poor to non-existent. After several rounds of refinement and model building, the finished structures look quite good, have a consistent sequence assignment, and have Rwork in the high teens and Rfree in the low 20s. THE PROBLEM: It is the 2.8 Å complex that has the problem. We used Moleman2 to evaluate the B-factors for the 4 domains in the 8 monomers in the ASU. When we compiled the numbers, we noticed that Moleman2 and phenix.refine gave different numbers for the protein atoms for chain B in the 2.8 Å complex (6152 versus 6289). We checked the PDB and confirmed that there are 6152 protein atoms in chain B; the other 7 chains show no differences between the programs. So where did phenix.refine get 6289 protein atoms when only 6152 protein atoms are input for chain B? The number of residues are correct (780). Adding to the confusion, there are truncated residues in each of the 8 chains. In the phenix.refine output attached below, the PDB file is being read in. For chain A, the number of atoms and the number of residues are correct, as well as the number of incomplete residues ({'truncation_to_alanine': 14}). However, for chain B, the number of incomplete residues ({'truncation_to_alanine': 21}) should be 37. Any ideas? Thanks, Michael **************************************************************** R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334 Email: garavito(a)msu.edu **************************************************************** phenix.refine output: Monomer Library directory: "/usr/local/phenix-1.7-650/chem_data/mon_lib" Total number of atoms: 51463 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 6289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6289 <==== matches PDB file Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 14} <==== MATCHES PDB file Link IDs: {'PTRANS': 34, 'TRANS': 746} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan2': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 . . . . Chain: "B" Number of atoms: 6236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6236 <==== DOES NOT MATCH PDB file 780 residues with 6152 atoms Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 21} <==== 37 truncation_to_alanine Link IDs: {'PTRANS': 34, 'TRANS': 745} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved chain link planarities: 2 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLN:plan2': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49

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Detecting and dealing with Pseudotranslation and/or twinning
by Hamaoka, Brent 12 May '11

12 May '11

I’ve been working on a troublesome protein structure. The native protein forms crystals that diffract to 2.75A and belong to P212121 (55.179 64.316 233.748 90.000 90.000 90.000) with 4 molecules in the ASU. I have 3 versions of the same protein where selenomethionine mutations are incorporated at different positions. Interestingly, these mutations cause the protein to form crystals belonging to C2221 (56.130 64.665 240.854 90.000 90.000 90.000). Looking back at the native datasets, Xtraige indicates the largest Patterson peak is (0.5, 0.486, 0), height is 11.8% of the origin peak, and p_value(height) is 0.08549, which is just outside of the threshold for being identified as containing pseudotranslation. Datasets from a couple of the selenomet incorporated crystals yield diffraction to ~3.5A and anomalous signal to ~6.7A. Some of the datasets give a solution with reasonable maps, but the best maps are achieved from combining MAD/SAD selenomet datasets and one from a mercury derivatized crystal using the ‘group’ command in Phenix. --------------------------------------------------------------------------- 5: STEP: finished Top solution: # 39 Dataset #0 BAYES-CC: 69.2 +/- 13.4 FOM: 0.6 Built: 219 Side-chains: 44 Chains: 9 CC: 0.74 Score type: SKEW CORR_RMS NCS_OVERLAP Raw scores: 0.41 0.82 0.00 100x EST OF CC: 69.17 43.34 31.25 --------------------------------------------------------------------------- Maps from this solution show connected electron density that looks like helices, consistent with the predicted secondary structure. Strangely, there is absolutely no side-chain density, only c-beta at most. I can build a poly-ala model into the map and the distances between the heavy atom sites appear correct based upon the known positions of the selenomethionines and the single cysteine in the protein sequence. However the model does not refine. R-free starts and remains near 0.45. I’ve tried indexing in lower symmetry space groups (P2, C2, P1) and re-solving by molecular replacement, but the refinement still fails. Xtriage does not indicate twinning. Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws <I^2>/<I>^2 : 2.305 <F>^2/<F^2> : 0.758 <|E^2-1|> : 0.788 <|L|>, <L^2>: 0.501, 0.333 Multivariate Z score L-test: 1.643 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not necessarily exclude it. One possible clue as to what is going on comes from analysis of SOLVE results. I was analyzing whether SOLVE/PHENIX solutions were related with one another by various origin shifts and came across one particular SOLVE run from a SeMet SAD dataset in C2221 that gave good statistics for a solution FOM=0.57, Z-score=20.26, peak height between 7.1 and 10.8 for 4 SeMet sites to 3.8A). The maps, however, looked poor. What was interesting, though, was that 2 of the Se sites matched well with where I was expecting the Se sites in one molecule in the asymmetric unit. The other two matched with where I would expect the sites in the other molecule when the model is shifted by one half the unit cell distance along the ‘a’ or ‘b’ axis. I’d appreciate any advice as to what might be happening, and how might I go about detecting the problem, and how to dealing with the data? Brent Hamaoka UC San Diego 9500 Gilman Drive 0375 La Jolla, CA 92093

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problem with version 1.7.1-743 linux
by Daniel PANNE 12 May '11

12 May '11

I get the following error only in 1.7.1-743 but not in 1.7_650. Any idea? Thanks, Daniel ******************************************************************************* ERROR: Unused parameter definitions: refinement.main.compute_optimal_errors (file "P1_refine_rigid.eff", line 257) refinement.pdb_interpretation.peptide_link.use_finite_differences (file "P1_refine_rigid.eff", line 514) refinement.secondary_structure.h_bond_restraints.substitute_n_for_h (file "P1_refine_rigid.eff", line 977) refinement.secondary_structure.h_bond_restraints.restrain_initial_values (file "P1_refine_rigid.eff", line 983) refinement.secondary_structure.h_bond_restraints.sigma (file "P1_refine_rigid.eff", line 984) refinement.secondary_structure.h_bond_restraints.slack (file "P1_refine_rigid.eff", line 985) refinement.secondary_structure.h_bond_restraints.h_o_distance_ideal (file "P1_refine_rigid.eff", line 986) refinement.secondary_structure.h_bond_restraints.h_o_distance_max (file "P1_refine_rigid.eff", line 987) refinement.secondary_structure.h_bond_restraints.n_o_distance_ideal (file "P1_refine_rigid.eff", line 988) refinement.secondary_structure.h_bond_restraints.n_o_distance_max (file "P1_refine_rigid.eff", line 989) ******************************************************************************* Sorry: Unused parameter definitions: Please check the input file(s) for spelling errors and obsolete parameter definitions. To disable this error message, add --unused_ok to the command line arguments.

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Technician Position available in Milan
by Sebastiano Pasqualato 12 May '11

12 May '11

Dear all, a technical position is available to work in the Crystallography Unit of the IFOM-IEO-Campus in Milan. (http://www.ifom-ieo-campus.it/joinus/detail_jobs.php?docuID=1566) The position is available immediately, and will be granted until March 2012. We are looking for a person who will be involved in the general management of the Unit's instrumentation, and who will take care of gathering samples from the Unit users, set up crystallization trials and perform biophysical experiments. Hence, we look for a person capable of independently organizing her/his work and with a great attitude to relate with people and work in a team. To apply, please send your CV, together with the name of at least one referee. Informal inquiries are welcome. cheers, Sebastiano PS: sorry for the double posting to those subscribed to both mailing lists. -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990

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Multiple pdb entries in phenix.fmodel
by zhangh1＠umbc.edu 11 May '11

11 May '11

Hi, I just wonder for the huge systems which have been split multiple pdb entries, if I provide all the pdb files in a single script of phenix.refine: phenix.fmodel A.pdb B.pdb C.pdb data.mtz whether everything will go correctly? Or I have to merge them into a single pdb and renumber all atoms sequentially? Thanks!

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Re: [phenixbb] mr_rosetta
by Thomas C. Terwilliger 11 May '11

11 May '11

Hi Jermaine, I am sorry for the trouble! I am wondering if rosetta is working quite right? Can you possibly run the regression tests on mr_rosetta: phenix_regression.wizards.test_command_line_rosetta_quick_tests and see if that helps diagnose the problem? All the best, Tom T >> I have been trying a standard run of mr_rosetta and I have stopped at the >> same point (output below). 32 folders were created in the >> GROUP_OF_RESCORE_MR_ROSETTA_1 folder and the mr_rosetta.log files all say >> that saved overall results to a .../results.pkl and the Run log file >> states >> that each job finished. But no further files were written in the Work >> folder >> under each RUN folder and I am assuming there should be a folder with my >> final 20 Rosetta models somewhere. Does this mean there was a failure in a >> subscript? >> ============================================================================== >> >> Starting sub-processes Group of rescore MR rosetta:Rescoring set of >> rosetta >> models... >> ============================================================================== >> >> Splitting work into 32 jobs and running with 4 processors using sh >> background=True in ....MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1 >> >> Starting job 1...Log will be: >> ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_1.log >> Starting job 2...Log will be: >> ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_2.log >> >> thanks, >> JJ >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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mr_rosetta
by Jermaine Jenkins 11 May '11

11 May '11

I have been trying a standard run of mr_rosetta and I have stopped at the same point (output below). 32 folders were created in the GROUP_OF_RESCORE_MR_ROSETTA_1 folder and the mr_rosetta.log files all say that saved overall results to a .../results.pkl and the Run log file states that each job finished. But no further files were written in the Work folder under each RUN folder and I am assuming there should be a folder with my final 20 Rosetta models somewhere. Does this mean there was a failure in a subscript? ============================================================================== Starting sub-processes Group of rescore MR rosetta:Rescoring set of rosetta models... ============================================================================== Splitting work into 32 jobs and running with 4 processors using sh background=True in ....MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1 Starting job 1...Log will be: ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_1.log Starting job 2...Log will be: ..../MR_ROSETTA_1/GROUP_OF_RESCORE_MR_ROSETTA_1/RUN_FILE_2.log thanks, JJ

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Low Resolution Density Modification Problems
by Ian Slaymaker 10 May '11

10 May '11

I am having a problem getting a decent DM map at lower resolutions (8, 10, 12, 20). We have a model for the data (R-factor ~34) at 6.6 A (the model is based on different higher resolution data), and when I try and do DM at anything worse than 6.6, the density no longer covers the model. Any suggestions would be appreciated. Ian Slaymaker USC <http://www-scf.usc.edu/%7Eslaymake/>

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Different R-free values
by Jerome Nwachukwu 10 May '11

10 May '11

Dear all: I find that phenix.refine reports a higher starting R-free than those stated for structures downloaded from the PDB. For instance, the R-free stated in the PDB = 0.287, using Polygon = 0.2880, but the Start R-free from phenix.refine = 0.3114 Is this usual, or is something seriously wrong? Thank you, -Jerome Jerome C. Nwachukwu, PhD Dept. of Cancer Biology The Scripps Research Institute-Florida 130 Scripps Way, 2C1 Jupiter, FL 33458

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error from loop fitting
by Kendall Nettles 09 May '11

09 May '11

I'm trying the loop fitting for the first time and keep getting this error: Reading in sequence probability info and matching to input PDB List of segments read from input PDB file: Segment 0 Start: 225 End: 380 ChainID: 'A' NO MATCH What should be in the sequence file? it is fasta format?it is the entire sequence, or just the loop? I've played with different combinations and keep getting the same error. Best regards, Kendall Nettles

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Diffraction anisotropy
by Ina Lindemann 06 May '11

06 May '11

Hi, I am refining a structure of 2.3A resolution. The R values with and without bulk solvent and anisotropic scale are quite different as you can see here: Start R-work = 0.3751, R-free = 0.5562 (no bulk solvent and anisotropic scale) Final R-work = 0.3741, R-free = 0.5557 (no bulk solvent and anisotropic scale) Start R-work = 0.2298, R-free = 0.2974 Final R-work = 0.2261, R-free = 0.2970 I checked the anisotropy of the data with different tools: Results from Xtriage: Maximum likelihood isotropic Wilson scaling ML estimate of overall B value of None: 39.25 A**2 Estimated -log of scale factor of None: -2.59 Maximum likelihood anisotropic Wilson scaling ML estimate of overall B_cart value of None: 50.10, 0.00, 0.00 50.10, -0.00 25.47 Equivalent representation as U_cif: 0.63, -0.00, -0.00 0.63, 0.00 0.32 Eigen analyses of B-cart: Value Vector Eigenvector 1 : 50.103 ( 0.71, 0.71, -0.00) Eigenvector 2 : 50.103 (-0.71, 0.71, -0.00) Eigenvector 3 : 25.473 (-0.00, 0.00, 1.00) ML estimate of -log of scale factor of None: -2.57 Correcting for anisotropy in the data Results from PHASER: Principal components of anisotropic part of B affecting observed amplitudes: eigenB (A^2) direction cosines (orthogonal coordinates) 8.178 0.9961 0.0879 0.0000 8.178 -0.0879 0.9961 0.0000 -16.357 -0.0000 -0.0000 1.0000 Anisotropic deltaB (i.e. range of principal components): 24.535 Results from Ctruncate: ANISOTROPY CORRECTION (using intensities): Anisotropic scaling (orthogonal coords): | -0.2272 -0.0000 -0.0000 | | -0.0000 -0.2272 0.0000 | | -0.0000 0.0000 0.4543 | Anisotropic U scaling (fractional coords): | -4.451e-05 -5.622e-23 -1.266e-21 | | -5.622e-23 -4.451e-05 -8.929e-22 | | -1.266e-21 -8.929e-22 4.717e-06 | Anisotropic B scaling (fractional coords): | -3.514e-03 -4.439e-21 -9.995e-20 | | -4.439e-21 -3.514e-03 -7.050e-20 | | -9.995e-20 -7.050e-20 3.725e-04 | Eigenvalues: 0.7728 0.7728 1.4543 Eigenvalue ratios: 0.5314 0.5314 1.0000 Resolution limit in weakest direction = 3.156 A Now I am not sure about the severeness of anisotropy and the necessary procedure and would be very pleased if anyone could help. The electron density maps look okay related to the resolution. Has anyone experience with the diffraction anisotropy server or ellipsoidal truncation with data with comparable anisotropy? Thank you for your help in advance Ina Ina Lindemann Philipps-Universität Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908

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phenix.mr_rosetta error
by Jermaine Jenkins 05 May '11

05 May '11

Hi, I am trying to use phenix.mr_rosetta supplying a local.hhr file and using only the top alignment which is an NMR structure and the pre_refine option. It finishes the mr.model_preparation and writes out two pdbs ( _sculpt and _chain that each have 10 ensembles) but then writes out a empty alignment.ali file (should be 100% identity between the template and the search model). Below is the error I get in the RUN_1.log file. Wrote dummy alignment to /pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali ******************* ERROR ENDING *************** Sorry, the alignment file ['/pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali'] does not have enough lines (6 required, 0 found): Note: last line needs to be '--' ******************* ERROR ENDING *************** Sorry, the alignment file ['../pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali'] does not have enough lines (6 required, 0 found): Note: last line needs to be '--' Thanks, JJ

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Off topic: Apologize for linkedin invitation accident
by Nian Huang 03 May '11

03 May '11

Dear fellows, I am really sorry for the massive invitations from my linkedin account. I was certain that I skipped the sending invitation step from my contact lists and I am not sure how it could still happen in the end. Please delete those emails as you wish and I thank the people who have already added me to the connection. Nian Huang, Ph.D. Dept. of Biochemistry UT Southwestern Medical Center

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Invitation to connect on LinkedIn
by Nian Huang via LinkedIn 03 May '11

03 May '11

LinkedIn ------------Nian Huang requested to add you as a connection on LinkedIn: ------------------------------------------ Felix, I'd like to add you to my professional network on LinkedIn. - Nian Accept invitation from Nian Huang http://www.linkedin.com/e/rc00ja-gn8i47ba-4i/_D6v-a9jXU1vVlzLNqYGbefdvPFwhu… View invitation from Nian Huang http://www.linkedin.com/e/rc00ja-gn8i47ba-4i/_D6v-a9jXU1vVlzLNqYGbefdvPFwhu… ------------------------------------------ Why might connecting with Nian Huang be a good idea? Have a question? Nian Huang's network will probably have an answer: You can use LinkedIn Answers to distribute your professional questions to Nian Huang and your extended network. You can get high-quality answers from experienced professionals. http://www.linkedin.com/e/rc00ja-gn8i47ba-4i/ash/inv19_ayn/ -- (c) 2011, LinkedIn Corporation

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Sulfate ion on 2-fold axis
by J. Fleming 01 May '11

01 May '11

Hi all, I have a sulfate ion sitting on a 2-fold axis of symmetry. If I set all the atom occupancies to 0.5 and refine using phenix.refine (Phenix v. 1.5-2) the occupancies are changed to 0.00 for the sulfur, 1.00 for three of the oxygen's, and 0.72 for the fourth oxygen. Can anyone explain this? Thanks in advance, Jon

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Phenix version 1.7.1 released
by Paul Adams 29 Apr '11

29 Apr '11

The Phenix developers are pleased to announce that version 1.7.1 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical Interface ------------------- - New interfaces for: phenix.phase_and_build, phenix.mtz2map, phenix.french_wilson - Updates to the Structure comparison GUI, which now allows use of non-identical sequences, and results viewing in PyMol. - A plugin for running multiple sequence alignment Installers ---------- - Graphical installers for Macintosh (installs in /Applications) - Binary installer for 64-bit Mac Intel (OS 10.6 only) New Commands ------------ - phenix.french_wilson (new command): - Implements French & Wilson correction of negative and weak intensities (see Acta Cryst A34:517 [1978]) - outputs modified amplitudes in MTZ format - used internally by default in Phaser GUI and phenix.refine when intensities are provided - phenix.reciprocal_space_arrays (new command): - this tool takes a PDB model and a data file and outputs an MTZ file containing a number of arrays that are typically used in various crystallographic calculations, such as R-factors, maps, refinement targets, etc. The output arrays include: - Fmodel, Fcalc, Fmask, Fbulk, FOM, resolution, Hendrickson-Lattman coefficients (input original, computed from model and combined), FB_CART (overall anisotropic scale), input Fobs and Rfree-flags and more - phaser.brunett (new command): - automated molecular replacement using incremental exploration, with support for parallelization - quick SSM-superposition-based LLG evaluation for alternative models for the same component - "puzzle"-assembly of solutions for a more complete solution - novel space group determination algorithm that retains possible space groups until they are significantly outperformed by others - handles custom models (used without modification), templates (a PDB template and an alignment, Sculptor is run to create models from it) and homology searches (PDB and alignment obtained from homology search, currently HHPRED and BlastXML; data downloaded from EBI) Structure refinement -------------------- - New output MTZ file that contains original data, amplitudes used in refinement, and map coefficients (this replaces *_map_coeffs.mtz) - French and Wilson procedure automatically applied if intensities are input to refinement - Optional automatic rigid-body grouping by polymer chain (rigid_groups_mode=one_group_per_chain) - Reference model uses a "top-out" restraint potential with a smooth cutoff - Automatic determination of Saenger class for nucleic acid base pairs (if not provided by user) - Ability to run phenix.find_tls_groups internally to obtain atom selections - option: tls.find_automatically=True - Automatic non-bonded distance correction for H-bonded atoms Molecular Replacement --------------------- - phenix.mr_rosetta: - Bug fixes - Added web site with data used in Nature Rosetta+Phenix paper at: http://www.phenix-online.org/phenix_data/terwilliger/rosetta_2011/ - Added keyword include_solvation_energy=False to allow use of mr_rosetta for membrane proteins. - phenix.automr: - bug fix in residue number input, now allows four-digit IDs Ligands ------- - eLBOW: - Geometries can be generated using CSD Mogul substructure searches of experimental geometries. Estimated standard deviations of the bonds and angles are also included in the restraints file. Visualization ------------- - KiNG (phenix.king): - Improved opening multiple electron density maps: tiered windows, with automatic deciphering of file name to preset sigma levels and colors. - Added -phenix command line option to preset map colors to be more like Coot. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Kathleen Moody [ KLMoody(a)lbl.gov ][ 1-510-495-2506 ] --

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TLS group definition
by Andres Palencia 28 Apr '11

28 Apr '11

Dear All, I am trying to refine using TLS parameter as in the attached file generated in ccp4. my protein contains a core part from where are inserted several domains. I am defining each of the insertions as a group and this is fine. The problem comes when I try to define the core protein (discontinuous residue ranges). As example, I want to define residues 1:230, 416:568, 629:794 in chain A of the protein; and in the same group I would like also to include 3 bases of RNA, bases 84-87 of chain B. I have seen several questions related to TLS definitions in the archive mailing list, including an answer from Anastasis Perrakis with files attached which I can not extract, but so far I have not find the solution. Could anybody help on that? thanks in advance, Andrés Palencia -- Andres Palencia, PhD Protein RNA Group EMBL Grenoble Outstation 6 rue Jules Horowitz BP181, 38042 Grenoble Cedex 9, France email: palencia(a)embl.fr phone: + 33 (0)476 20 7860(office)/ + 33 (0)476 20 7014(lab) fax: + 33 (0)476 20 7199 http://www.embl-grenoble.fr/

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phenix.maps
by Bradley Hintze 27 Apr '11

27 Apr '11

This shows my ignorance about mtz files. I'm having trouble with phenix.find_helices_strands. I got 3kat.mtz from Pavel's database. I run: $ phenix.find_helices_strands 3kat.mtz labin="LABIN FP=2FOFCWT PHIB=PH2FOFCWT" and get: PHENIX find_helices_strands Wed Apr 27 13:12:19 2011 Commands: phenix.find_helices_strands 3kat.mtz labin=LABIN FP=2FOFCWT PHIB=PH2FOFCWT # find_helices_strands # # Find secondary structure in a map defined by map coeffs in an input mtz file. # Type phenix.doc for help Input map resolution is 3.1 A Labin line will be: LABIN FP=2FOFCWT PHIB=PH2FOFCWT To change it modify this by specifying FP= and PHIB= [and optionally FOM=] like this: labin="LABIN FP=2FOFCWT PHIB=PH2FOFCWT" Map from: TEMP_3kat.mtz using labin LABIN FP=2FOFCWT PHIB=PH2FOFCWT NOTE: ratio_trace_extra increased to 1.3 A as dmin > 3.0 NOTE: rad_sep_trace increased to 0.6 A as dmin > 3.0 Fixing sampling interval rad_sep_trace= 0.6 A Optimizing CA-CA tolerance to obtain ratio of 4.0 for nonamers:atoms Tracing chains at resolution of 3.1 A CCP4: Error in label assignments in LABIN

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Question regarding phenix.fmodel
by zhangh1＠umbc.edu 26 Apr '11

26 Apr '11

Hi, According to the instruction, phenix.fmodel was supposed to calculate Fc only; however, when I try the following 2 scripts, they ended up with different Fc values (at the same hkl point): 1. phenix.fmodel ${PDB} high_resolution=XX 2. phenix.fmodel ${PDB} ${MTZ} The instruction says (2) will output Fcalc that will match the set of Miller indices of the data in reflection_data.mtz file, so I thought 1 and 2 should have the same values at the same hkl points... One more question about fmodel. I have 2 models with different sizes, and want to compare their Fc in the same scale. If I use (1), there will be no scaling by default I think, so the Fc results can be directly compared, right? (A most direct way would be checking the Fc at h0k0l0 point and see whether they are proportional to the molecular size, but it seems phenix.fmodel will ignore this point even I expicitly add it to the MTZ file.) Thanks! Hailiang

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Residue number error after autoMR or PhaserMR
by Zhang yu 23 Apr '11

23 Apr '11

Hi, When I run MR in Phenix, I found that there is a numbering error in the solution PDB file The error is that Phenix numbers residues from 0 again when the residue numbers are over 999, though they belong to the same chain. For example "ATOM 11504 N HIS C 999 -37.389 50.436 57.144 1.00 56.62 N ATOM 11505 CA HIS C 999 -36.908 51.569 57.924 1.00 60.55 C ATOM 11506 C HIS C 999 -37.438 51.479 59.337 1.00 61.73 C ATOM 11507 O HIS C 999 -38.648 51.484 59.549 1.00 60.99 O ATOM 11508 CB HIS C 999 -37.382 52.895 57.326 1.00 63.09 C ATOM 11509 CG HIS C 999 -36.353 53.577 56.478 1.00 66.67 C ATOM 11510 ND1 HIS C 999 -35.280 52.912 55.925 1.00 68.12 N ATOM 11511 CD2 HIS C 999 -36.247 54.865 56.070 1.00 68.95 C ATOM 11512 CE1 HIS C 999 -34.559 53.762 55.214 1.00 69.21 C ATOM 11513 NE2 HIS C 999 -35.122 54.953 55.285 1.00 69.80 N ATOM 11514 N MET C 0 -36.544 51.378 60.309 1.00 64.17 N ATOM 11515 CA MET C 0 -36.992 51.355 61.688 1.00 66.45 C ATOM 11516 C MET C 0 -37.290 52.797 62.083 1.00 68.10 C ATOM 11517 O MET C 0 -37.018 53.716 61.302 1.00 68.58 O ATOM 11518 CB MET C 0 -35.903 50.763 62.605 1.00 67.35 C ATOM 11519 CG MET C 0 -36.051 49.272 62.997 1.00 67.14 C ATOM 11520 SD MET C 0 -36.534 48.947 64.735 1.00 65.84 S ATOM 11521 CE MET C 0 -35.169 49.744 65.675 1.00 66.20 C ATOM 11522 N VAL C 1 -37.840 53.015 63.272 1.00 69.46 N ATOM 11523 CA VAL C 1 -38.160 54.373 63.711 1.00 69.99 C ATOM 11524 C VAL C 1 -36.911 55.251 63.875 1.00 70.28 C ATOM 11525 O VAL C 1 -37.029 56.452 64.122 1.00 70.20 O ATOM 11526 CB VAL C 1 -38.908 54.379 65.057 1.00 70.57 C ATOM 11527 CG1 VAL C 1 -40.322 53.847 64.873 1.00 71.16 C ATOM 11528 CG2 VAL C 1 -38.148 53.537 66.061 1.00 70.54 C" Does anyone has idea about it? Thanks Yu Zhang

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fwd: Workshop on "Soft X-ray Crystallography" at the APS, May 4, 2011
by Nathaniel Echols 22 Apr '11

22 Apr '11

---------- Forwarded message ---------- From: Bi-Cheng Wang <wang(a)bcl1.bmb.uga.edu> To: phenixbb(a)phenix-online.org Date: Fri, 22 Apr 2011 12:13:02 -0400 Subject: Workshop on "Soft X-ray Crystallography" at the APS, May 4, 2011 We would like to call your attention to a workshop associated with the upcoming 2011 APS Users Meeting, which will be held on May 4, 2011 at the APS, Argonne National Laboratory, USA. The title of the workshop is “Soft X-ray Crystallography”. You may find the workshop program at http://2011usersmeeting.conference.anl.gov/APSWK1Agenda.htm The web links for meeting registration and the application for a permit to enter the Argonne National Laboratory are: https://2011usersmeeting.conference.anl.gov/register http://www.aps.anl.gov/Users/Site_Access We hope you will be able to attend the APS Users Meeting and our workshop. All the best, B.C. Wang, John Rose, Gerd Rosenbaum and John Chrzas

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