- phenixbb - phenix-online.org

Ligand / Loop occupancy refinement
by Antony Oliver 19 Sep '11

19 Sep '11

Dear all, Apologies if this has been covered already in a previous post — but I can't find a suitable response in the archive. We have the following situation... We have soaked a ligand into an apo-crystal, collected diffraction data, and solved the structure. What is apparent from the electron density, is that the ligand isn't in the crystal at full occupancy, it's roughly about 70-80%. However, as the ligand binds, it causes a small conformation change in the active site of the protein, altering the position of around 4 amino acids. What I want to do, and can't quite get phenix.refine to do is the following... Refine the occupancy of the ligand (chain C resname LIG) with the "A" conformation of the active site residues (which should be the same, as they are mutually dependent) — and then refine the occupancy of the "B" conformation of the active site residues — which should all theoretically add up to a total of 1. Could anyone help me with how the occupancies / constrained_group parameters should be set up in this case? With thanks, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk<mailto:[email protected]> tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512

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bulk solvent mask question
by Laurie Betts 16 Sep '11

16 Sep '11

I notice that during refinement of a MR solution for a protein (search model is 100% homologous to target), a very large ligand-binding cavity (as much as 20 A wide in some parts) in my protein gives weak positive difference density for a ligand soaked into the crystals, unless I turn off bulk solvent modeling. Then the fo-fc difference density is quite strong (2.6 Angstrom data). I think this is due to part of the cavity being included in bulk solvent? Can I edit the mask easily, or flag parts of the protein as NOT exposed to solvent? Thanks Laurie Betts

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Refinement with optimize weights
by Ankit Gupta 16 Sep '11

16 Sep '11

Hello Forum, I am using Phenix 1.7.1-743 to refine my structure. My R/Rfree values for a 2.5 A structure were 0.22/0.305. I used optimize weights along with TLS and the R/Rfree values improved to 0.23/0.29. I wanted to know what parameters should I use for subsequent refinement. I read on phenix bb that one needs to fix the wxc_scale and wxu_scale. Is this correct? What values should be used for these parameters after running optimize wxc/wxu weights. Is there any place where I can get starting values for my future refinement? Also, I would like to know what Fix X-ray/stereochemistry weight and Fix X-ray/ADP weights are for? Thanks for the help.

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Phenix.refine distorts geometry during rigid body refinement
by Ian Slaymaker 14 Sep '11

14 Sep '11

I am bringing a PDB refined in Refmac back to phenix.refine. After an initial rigid body refinement to compare numbers (one chain per group), the geometry (specifically the bond length rmsd) had surprisingly increased. Phenix.validate confirmed the Refmac (initial) geometry numbers and then afterwards confirmed the distorted geometry. What is strange is that when opened in COOT, the initial and final models are completely super imposed. REMARK Start: r_work = 0.3375 r_free = 0.3624 bonds = 0.006 angles = 0.768 REMARK Final: r_work = 0.3379 r_free = 0.3626 bonds = 0.145 angles = 1.019 can you help me figure out what is going on here? These are the final few refinements of a 4.1 A structure. Thanks, Ian

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Linux kernel version 3.0 detection
by Ben Eisenbraun 14 Sep '11

14 Sep '11

Hi, Robert Campbell at Queens pointed out to me that the "machine_type" script bundled with PHENIX doesn't understand the new version 3.0 linux kernel strings. He tweaked his local copy for testing purposes on a Debian testing machine, and just forcing the 3.0 version to use the 2.6 binaries worked: case "$KERNEL" in 2.4.*) kernel_version=2.4 ;; 2.6.*) kernel_version=2.6 ;; 3.0.*) kernel_version=2.6 ;; *) kernel_version="$KERNEL" ;; esac I haven't tested it myself. It looks like Fedora 16 and Ubuntu 11.10, both targeted for November releases, will be using the new 3.0 kernel. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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Multiple conformations of disulfide
by Matthew Merski 13 Sep '11

13 Sep '11

Hello, I am trying to refine a surface cys that is alkylated by beta-mercaptoethanol (BME). The BME appears to have two poses and I am having trouble with getting phenix to understand the restraints. When I give the BME two conformations I get the error: Sorry: No atom selected: "chain A and resname ABME and resid 165 and name S2" My link_params file looks like this: refinement.geometry_restraints.edits { drgA_selection1 = chain A and resname ABME and resid 165 and name S2 bond { action = *add atom_selection_1 = $drgA_selection1 atom_selection_2 = $cys215_selection distance_ideal = 2.05 sigma = 0.02 slack = None } Not calling it ABME of course results in a non-unique atom error. Thanks for your help. Matthew Merski UCSF Shoichet Group

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phenix.refine restraint
by Simon Kolstoe 12 Sep '11

12 Sep '11

Dear phenixbb, I'm trying to constrain a ligand-metal bond that is continuously getting altered by phenix.refine (my data's only 3.2A). I've added the following restraint but it just doesn't seem to be holding the bond length during refinement. Is there a different way of telling phenix.refine not to alter this distance? (I'm doing it all on the command line & by editing the .def file). refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name CA and chain X and resname CA and resseq 1 atom_selection_2 = name O1 and chain L and resname ROC and resseq 1 distance_ideal = 2.380000 sigma = 0.100 } } Thanks, Simon --------------------------------------------------------------- Dr Simon Kolstoe Laboratory for Protein Crystallography Centre for Amyloidosis & Acute Phase Proteins UCL Medical School Rowland Hill Street, London NW3 2PF Tel: 020 7433 2765 http://www.ucl.ac.uk/~rmhasek ---------------------------------------------------------------

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phenix.refine and ice rings.
by Francis E Reyes 08 Sep '11

08 Sep '11

Hi phenixer's / developers. A quick question: Curious, how are spots that lie on ice rings dealt with? At which step? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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FOM in output MTZ file from phenix.refine
by Joern Krausze 08 Sep '11

08 Sep '11

Dear all, there is no FOM comlumn in my output MTZ file from phenix.refine. According to the documentation, the MTZ with FOM should be written out by default. I did not find any option that would trigger FOM inclusion. What can I do to include FOM? Thanks, Joern ****************************************** Address: Joern Krausze Molecular Structural Biology Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany Email: joern.krausze(a)helmholtz-hzi.de Phone: +49 (0)531 6181 7023 (office) +49 (0)531 6181 7020 (lab) ****************************************** Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Heiko Gevers, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Ulf Richter, MBA Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Postdoc Position at LBNL
by Nicholas Sauter 07 Sep '11

07 Sep '11

Exploring New Horizons in Data Processing. The Computational Crystallography group at Lawrence Berkeley National Lab ( http://cci.lbl.gov) would like to recruit an outstanding postdoctoral scientist with a strong interest in the computational challenges at the forefront of structural biology. With synchrotron beamlines increasingly controlled automatically and remotely, and with CCDs being replaced by pixel-array detectors, software development is critical to future experimental success. Better algorithms are needed to realistically model the diffraction observed on the new detectors, and the blinding data acquisition speed will require a new focus on efficiency. Difficult challenges also remain for deriving structural information from free-electron laser experiments. Two years after first light at the LCLS, new research on data analysis has become increasingly vital. This position offers the opportunity to collaborate with Bay Area beamline developers at both the ALS and SSRL, and access to unprecedented data sets from LCLS nanocrystallography studies. Local resources include numerous groups developing crystallography methods, as well as expertise in computational hardware including graphics processing units. Software will be developed within an open-source paradigm, and is expected to have a worldwide influence on high-throughput structural biology. Candidates should have a recent Ph.D. in computational biology or a related field, as well as strong experience in instrumentation, software, or data analysis. Applications consisting of a statement of research interests, CV, list of publications, and three references should be submitted on the Web at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=73565 -- Nicholas K. Sauter, Ph. D. Computer Staff Scientist/Engineer Physical BioSciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 64R0121 Berkeley, CA 94720-8118 (510) 486-5713

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