SBGrid PHENIX 2016

Looking forward to seeing you at PHENIX 2016.

Software

We will be using PHENIX during the workshop but you may also want to install PyMOL, CCP4 (includes COOT), and any other tools you prefer to use. https://sbgrid.org/wiki/client_install

Reference Datasets

We have assembled a set of reference data for discussion during workshop.

You can download the data as a tarball here : Workshop2016Datasets.tar.bz2 - 37.5Mb

or

Workshop2016Datasets.zip - 37.5Mb

Directory names

  • kd : processing results from Kay Diederichs
  • sbdb : automated data reduction results
  • PDB CODE.fasta : sequence file from RCSB

See Archive directory structure below.

Images are not necessary but can be downloaded from the SBDB with:

rsync -av rsync://data.sbgrid.org/10.15785/SBGRID/<dataset number>  .

Dataset info

Each dataset includes a readme.txt file with a description.

Dataset #3 : X-Ray Diffraction data from Lin28/let-7d microRNA complex, source of 3TRZ structure, Zn-SAD dataset

Dataset #97 : X-Ray Diffraction data from Thermoanaerobacter tengcongensis SONO (H-NOX) in complex with dioxygen, source of 1XBN structure, MAD dataset collected at the iron edge

Dataset #111 : X-Ray Diffraction data from 'Spinach' RNA-chromophore complex, source of 4TS0 structure

Dataset #123 : X-Ray Diffraction data from HSV-2 gH/gL complex, source of 3M1C structure, A selenomethionine single-wavelength anomalous diffraction dataset

Archive directory structure

├── 111
│   ├── 4TSO.fasta
│   ├── kd
│   │   ├── CORRECT.LP
│   │   ├── XDS_ASCII.HKL
│   │   └── XDS.INP
│   ├── readme.txt
│   └── sbdb
│       ├── proc-0.mtz
│       ├── proc-1.mtz
│       ├── proc-2.mtz
│       └── proc-3.mtz
├── 123
│   ├── 3M1C.fasta
│   ├── kd
│   │   ├── CORRECT.LP
│   │   ├── XDS_ASCII.HKL
│   │   └── XDS.INP
│   ├── readme.txt
│   └── sbdb
│       ├── proc-0.mtz
│       ├── proc-1.mtz
│       ├── proc-2.mtz
│       └── proc-3.mtz
├── 3
│   ├── 3TRZ.fasta
│   ├── kd
│   │   ├── CORRECT.LP
│   │   ├── XDS_ASCII.HKL
│   │   └── XDS.INP
│   ├── readme.txt
│   └── sbdb
│       ├── proc-1.mtz
│       ├── proc-2.mtz
│       └── proc-3.mtz
└── 97
    ├── 1XBN.fasta
    ├── readme.txt
    └── sbdb
        ├── proc-1.mtz
        └── proc-2.mtz