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map error?
by Christian Roth 19 May '11

19 May '11

Dear all, I got a error message in the last round of phenix.refine which seesm to be related to map or mtz file creation (error.txt attached). I used the GUI and I unchecked the map creation option in ccp4 or Xplor before I started the run. I am not sure whats going wrong here. Please could you point me to the problem. Best regards Christian

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AutoSol
by Nora Cronin 19 May '11

19 May '11

Whilst I can input SAD SAD data ie two different SAD datasets using Group =1 and Group =2 with the "Wavelength" keyword, how do I input 2 different crystals using the "crystal_info" keyword which does not recognize Group = Inputting .sca unmerged anomalous data how do I input data for 2 different crystal_info keywords with different heavy atoms and different unit cells? thanks Nora Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5457 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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mr_rosetta on a supercomputer
by Patricia Amara 18 May '11

18 May '11

Hello, I have been trying to run phenix.mr_rosetta on a supercomputer where we are limited to 24h for parallel jobs and we have different queues for job mono. Thus to run we have two files. We do not really understand how the code proceeds with nproc so we just put 6 for now. When we sent it, it created 1000 jobs on MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1 it sent 10 jobs mono, but ran only 5 first than the other five. Then the job running the script hangs. when we looked at the log files in the MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1 directories it filled up only 4 if we re-run only 3 and never the same. do you have any idea what we're doing wrong? thanks in advance for your input Patricia Amara ps; Thus to run we have two files. One to send the script #!/bin/bash #MSUB -e ros1_%I.e #MSUB -o ros1_%I.o #MSUB -n 6 #MSUB -T 86400 cd /scratch/cont003/amara/Rosetta-NadA ./rosetta.run and the script itself: phenix.mr_rosetta \ seq_file=/scratch/cont003/amara/Rosetta-NadA/NADA.seq \ data=/scratch/cont003/amara/Rosetta-NadA/NadA-7-BM16-remote-no_ano-P21212-Rfree_shell.mtz \ search_models=/scratch/cont003/amara/Rosetta-NadA/model_2.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = /scratch/cont003/amara/Rosetta-NadA/aat000_03_05.200_v1_3.gz \ fragment_files = /scratch/cont003/amara/Rosetta-NadA/aat000_09_05.200_v1_3.gz \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies=3 \ space_group=p21212 \ use_all_plausible_sg=False \ max_wait_time=100 \ nproc=6 \ group_run_command= "/usr/share/lsf/7.0/linux2.6-glibc2.3-x86_64/bin/bsub -n 1 -q mono -W 03:00"

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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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