June 2012 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

6 8

links in phenix summary
by Christian Roth 04 Apr '13

04 Apr '13

Dear all, thanks to the phenix team which helped me a lot to resolve all issues regarding the correct link definitions. I have summarised a few things which one might consider if nonstandard links are necessary. Try phenix ready set to get your links out of the pdb. Do not forget to change the possible LINKR to LINK! Inspect the links and decide if they are useful! Peptide links are automatically incorporated if residues are close (inspect geo file) Non standard peptide links could be created using using an now available alpha release script: elbow.ligand_linking model.pdb Inspect the generated cif file and correct angles and incorporate dihedrals and so on if necessary. Sugar links which exists in the mon_lib.cif should be incorporated using the apply_cif link option like refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain B and resname GLC and resseq 1 residue_selection_2 = chain B and resname GLC and resseq 2 } According to the link definition the C1 oxygen of the following sugar with the higher number must be removed. The automatic incorporation of sugar links will be probably soon available in phenix. Nigel is already working on this. If one want use hydrogens in the refinement, they have to be added previously with ready_set and afterwards the OH4 sugar hydrogen has to be removed before the refinement. For links with symmetry related atoms the symmetry operator must be included in a custom bond definition efinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = -x,y,-z distance_ideal = 2.2 sigma = 0.01 } } The operator can be obtained using iotbx.show_distances your.pdb > all_distances Search for keyword "sym" or from Coot clicking on the symm option. Coot print out the operator and the translation term separately. Both has to be merged in the final operator used in phenix! Christian

3 2

Postdoctoral Fellow & Scientific Officer / Higher Scientific Officer Positions at ICR, London, UK
by Sebastian Guettler 29 Jun '12

29 Jun '12

Dear PHENIX Community, We are currently looking for two motivated researchers to join our new, exciting research programme on the regulation and functions of ADP-ribosyltransferases: one Scientific Officer / Higher Scientific Officer and one Postdoctoral Fellow. Please see the job descriptions for the two positions and instructions on how to apply below. Best wishes, Sebastian Postdoctoral Fellow & Scientific Officer / Higher Scientific Officer Positions at ICR, London, UK In the Divisions of Structural and Cancer Biology of the Institute of Cancer Research (ICR; http://www.icr.ac.uk), our new team led by Dr. Sebastian Guettler has a vacancy for a Scientific Officer or early-career Higher Scientific Officer and a Post-doctoral Training Fellow. Research in the Divisions of Structural and Cancer Biology focuses on the functional, biochemical, and structural characterisation of cellular processes relevant to cancer and cancer therapy. The Division of Structural Biology, where the laboratory will be physically based, has managed facilities for protein crystallography (crystallisation robots, x-ray diffractions systems), cryo-electron microscopy and protein production with expertise in multi-subunit expression systems (bacterial, yeast and insect cell expression, including a 60-litre fermentor). The Division is also well equipped with instrumentation for biophysical analysis (e.g., ITC, fluorescence-based methods, multi-angle light scattering). The Division of Cancer Biology provides a state-of-the-art infrastructure for mammalian cell culture, imaging, mammalian genetics, chemical biology and proteomics. Position 1: Post-doctoral Training Fellow (job reference number 1257974) Closing date of vacancy: 6 July 2012 Starting date of position: mid-October / early November 2012 Division: Structural Biology & Cancer Biology Team: Guettler Group Type of contract: fixed term Length of contract: 3 years in the first instance Salary range: £27,536 to £33,852 p.a. inclusive (depending on previous post-doctoral experience) Work location: London (Chester Beatty Laboratories, Chelsea) The successful applicant will undertake biochemical, crystallographic and functional studies on members of the ADP-ribosyltransferase (or “PARP”) family of proteins and their regulators. Our goal is to gain insight into the control and cellular roles of these enzymes with a specific interest in ADP-ribosyltransferase-dependent signalling processes linked to cancer. Applicants should possess a PhD (or equivalent) in biochemistry or molecular biology and a sound knowledge of protein purification for structural analyses. Experience with recombinant DNA techniques, protein expression and purification as well as protein crystallography is essential. Experience in mammalian cell culture, enzymology or protein production in insect cells (MultiBac) would be of advantage. For further details and instructions on how to apply, please refer to our online vacancy and recruitment site at http://www.icr.ac.uk/jobsearch, quoting job reference number 1257974 for this position. While applications need to be placed via our online system, informal inquiries can be sent to Dr. Sebastian Guettler at sebastian.guettler(a)icr.ac.uk. Position 2: Scientific Officer / Higher Scientific Officer (job reference number 1260528) Closing date of vacancy: 20 July 2012 Starting date of position: mid-October / early November 2012 Division: Structural Biology & Cancer Biology Team: Guettler Group Type of contract: fixed term Length of contract: 3 years in the first instance Salary range: £23,000 to £29,545 p.a. inclusive (depending on skills and experience) Work location: London (Chester Beatty Laboratories, Chelsea) The objective of this post will be to provide support within Dr. Guettler's laboratory for research into the structure and function of proteins. The post holder will work as a member of a multidisciplinary team investigating the functions and regulation of ADP-ribosyltransferases. The work will involve the production and purification of proteins and protein complexes, their characterisation, crystallisation and functional analysis. Applicants should minimally possess a BSc (or equivalent) in molecular biology, biochemistry or cell biology. Experience in molecular cloning, recombinant protein expression in E. coli and large-scale, crystallisation-grade protein purification is essential. Experience with protein production in insect cells (MultiBac) and mammalian cell culture would be of advantage. For further details and instructions on how to apply, please refer to our online vacancy and recruitment site at http://www.icr.ac.uk/jobsearch, quoting job reference number 1260528 for this position. While applications need to be placed via our online system, informal inquiries can be sent to Dr. Sebastian Guettler at sebastian.guettler(a)icr.ac.uk. 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.

1 0

k_sol and b_sol
by Luca Pellegrini 28 Jun '12

28 Jun '12

Hello, Where do I find the minimised values of k_sol and b_sol in phenix.refine? For some reason, they are not included in REMARK 3 of the pdb file after refinement, and I can't find them in the log file. Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

2 1

Incorrect solvent modelling in Phenix.refine?
by David Briggs 27 Jun '12

27 Jun '12

Hi all, I'm refining a couple of structures of the same protein (well, point mutants) and I am consistently seeing large (6sig) negative difference map peaks within some cavities within my protein, present in both the datasets. As far as I understand, this is because the bulk solvent scaling parameters are either incorrect, or being incorrectly applied. I have tried a few things like applying the "Refine solvent mask (slow)" options, all to no avail. Resolution is 2.2Å and 2.5Å. Experimental phasing, Xtriage reports no abnormalities in the data. Is there anything that I am missing? Do I need to worry about this? Regards, Dave ============================ David C. Briggs PhD Father, Structural Biologist and Sceptic ============================ University of Manchester E-mail: david.c.briggs(a)manchester.ac.uk ============================ Webs : http://flavors.me/xtaldave Twitter: @xtaldave Skype: DocDCB ============================

2 1

Error in phenix.autobuild
by Tanner, John J. 27 Jun '12

27 Jun '12

Can anyone shed light on the error below? The situation is that I have a ~90% complete model from refinement (r_work = 0.2415, r_free = 0.3167), and I want phenix.autobuild to build the rest of the structure. I issued this command: phenix.autobuild data=../ccp4/DrPRODH3-6_1_scala2.6Ang.mtz model=Refine_9/DrPRODH_refine_9.pdb seq_file=../seq/DrPRODH-noMet1.fasta rebuild_in_place=False nproc=3 I got this error: [tannerjj@europa AutoBuild_run_2_]$ tail -n20 AutoBuild_run_2_1.log Output space group: P 1 21 1 (No. 4) Columns of data in AutoBuild_run_2_/refinement_PHX.mtz: H K L FreeR_flag F_DrPRODH3-6 SIGF_DrPRODH3-6 Unit cell: (46.806, 95.875, 70.504, 90, 107.733, 90) Space group: P 1 21 1 (No. 4) Using AutoBuild_run_2_/refinement_PHX.mtz for refinement Correcting data file /titan/tanner/DrPRODH/ccp4/DrPRODH3-6_1_scala2.6Ang.mtz for anisotropy and writing to AutoBuild_run_2_/aniso_data_PHX.mtz Getting overall aniso B from datafile... *************ERROR ENDING ******************* **************************************** AutoBuild Input failed iotbx InternalError: /net/longnose/scratch2/phenix/phenix-1.7.3-928/cctbx_project/iotbx/mtz/dataset.cpp(97): IOTBX_ASSERT(strlen(label) < sizeof(column_ptr->label)) failure. **************************************** *************ERROR ENDING *******************

3 4

occupancy group definition
by Christian Roth 26 Jun '12

26 Jun '12

Dear All, I have tried an occupancy refinement for a partially modifed residue. I have split the residue in altloc A and B and the modification (PMSF) is attached on B. I included the PMS moiety as part of the residue and gave them altloc B. I created the cif link. The refinement resulted in a strange mixture of occupancys for PMS around 0.8 and both Serins 0.23 an 0.77. So PMS is not part of the residue. I am not sure about the correct syntax for the constrained group. At the moment I have used constrained_group { selection = chain A and resseq 130 and altloc A selection = chain A and resname PMS and altloc B } However the Serine pat of altloc B refines to a value not compatible to the PMS values or the Altloc A value of the serine. How do I incorporate the altloc B for the serine? Thanks in advance for your help Christian

2 3

geometry weight help
by 周文昌 25 Jun '12

25 Jun '12

Dear all, Last week, I played a little bit with geometry weight in phenix refinement. When I check the log file, what I found is that if I use wxc_scale and fix_wxc in my refinement, actually phenix will ignore the wxc_scale, while if I only use wxc_scale, phenix will follow the value specified in the command line, but the wxc value will change from one macro cycle to another cycle. Below shows one of my examples in which the wxc_scale values are ignored when I use wxc_scale and fix_wxc at the same time. Anyone has similar problems? Thanks for all your considerations. ################## Command line arguments: "../new-unique.mtz" "../3tx8.pdb" "fix_rotamers=true" "strategy=individual_adp+individual_sites" "wxc_scale=0.01" "refinement.input.xray_data.labels=FP,SIGFP" "fix_wxc=10" "--overwrite" refinement.target_weights.wxc_scale = 0.01 refinement.target_weights.fix_wxc = 10 wxc_scale = 0.01 fix_wxc = 10 | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 10.000000 wxc_scale = 1.000 wc = 1.000 | ... ################## Wenchang

3 2

Diffractive Imaging Postdoctoral Scientist Opportunity
by Nicholas Sauter 25 Jun '12

25 Jun '12

I'd like to alert subscribers to an exciting postdoctoral scientist opportunity, using diffractive imaging to examine organelle-scale biological structures at the Linac Coherent Light Source. The job posting is listed at: http://academicemployment.chance.berkeley.edu/DetailsJobSearch.cfm?recordID… The advertised position is strongly oriented toward the development of computational methods. The successful candidate will join the group of Cheryl Kerfeld at UC Berkeley, and collaborate daily with scientists at LBNL. Informal inquiries may be directed to Nick Sauter, nksauter at lbl.gov Peter Zwart, phzwart at lbl.gov -- Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Physical Biosciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 64R0121 Berkeley, CA 94720-8118 (510) 486-5713

1 0

dihedral restraints problem with alternate conformations
by Benoît Masquida 25 Jun '12

25 Jun '12

I am having an issue refining 2 superimposed MES molecules A and B (morpholino ethane sulfonic acid, buffer seen in the density). phenix.refine works fine up to the end where it crashes because of the following error: Duplicate dihedral restraints: tor id: var_10 residue: MES, conformer "A" atoms: "HETATM 3993 O1 AMES T 1 .*. O " "HETATM 3994 C2 AMES T 1 .*. C " "HETATM 3995 C3 AMES T 1 .*. C " "HETATM 3996 N4 AMES T 1 .*. N+1" I can't see where is the conflict since all atoms have distinct labels and I provided the CIF file generated with phenix.elbow. What should I change to circumvent this problem? Thanks Ben

2 1