Automated Building of Secondary Structure Elements With Arp

Automated Building of Secondary Structure Elements With Arp. Navigator A Click-on Tutorial Joana Pereira and Tim Wiegels Hamburg

Where to go… Click! Joana Pereira Arp. Navigator Tutorials

ARP/w. ARP: Secondary Structure (albe) Click! Joana Pereira Arp. Navigator Tutorials

ARP/w. ARP: Secondary Structure (albe) Joana Pereira Arp. Navigator Tutorials

ARP/w. ARP: Secondary Structure (albe) Testcase: PDBID 1 o 14 (possible 1 -phosphofructokinase (TM 0828) from Thermotoga maritima) Residues: 2 x 331 (662) AA Resolution: 3. 2 angs. Files to use: 1 o 14. mtz MTS labels to use: F, PHIC, FOM Joana Pereira Arp. Navigator Tutorials

ARP/w. ARP: Secondary Structure (albe) Click! Joana Pereira Arp. Navigator Tutorials

ARP/w. ARP: Secondary Structure (albe) Choose one Joana Pereira Arp. Navigator Tutorials

1. Building of Helixes and Strands Click! Joana Pereira Arp. Navigator Tutorials

1. Building of Helixes and Strands Click! Joana Pereira Arp. Navigator Tutorials

1. Building of Helixes and Strands Choose one Joana Pereira Arp. Navigator Tutorials

1. 1. Start From MTZ File Click! Joana Pereira Arp. Navigator Tutorials

1. 1. 1. Input Files: MTZ File Click! Joana Pereira Arp. Navigator Tutorials

1. 1. 1. Input Files: MTZ File Search for the file Click! Joana Pereira Arp. Navigator Tutorials

1. 1. 1. Input Files: MTZ File Filled automatically (if defaults are available in mtz). If not, click on the button and search the list. Joana Pereira Arp. Navigator Tutorials

1. 1. 2. Resolution Click! Joana Pereira Arp. Navigator Tutorials

1. 1. 2. Resolution Limit resolution if you want to Resolution: 3. 2 Å Joana Pereira Arp. Navigator Tutorials

1. 1. 3. Required Parameters Total of 662 residues on the asymmetric unit Joana Pereira Arp. Navigator Tutorials

1. 1. 4. Run The Job Click! Joana Pereira Arp. Navigator Tutorials

1. 1. 4. Run The Job – Log File - Fragments found - Sec structure found - Etc. Click! Joana Pereira Arp. Navigator Tutorials

1. 1. 4. Run The Job – Live Model Building Joana Pereira Arp. Navigator Tutorials

1. 2. Start From MAP File Click! Joana Pereira Arp. Navigator Tutorials

1. 2. 1. Input Files: MAP File Does not need: - MTS labels As in 1. 1. 3. Does not allow: - Resolution restriction As in 1. 1. 4. Joana Pereira Arp. Navigator Tutorials Search for map file

2. Building of Helixes Only Click! Joana Pereira Arp. Navigator Tutorials

2. Building of Helixes Only As in 1. 1. or 1. 2 Joana Pereira Arp. Navigator Tutorials

Build Secondary Structure and Skeletons Quickly Click! Joana Pereira Arp. Navigator Tutorials

1. Load MTZ File Click! Joana Pereira Arp. Navigator Tutorials

1. Load MTZ File Search for the file Click! Joana Pereira Arp. Navigator Tutorials

1. Load MTZ File Click! Joana Pereira Arp. Navigator Tutorials

1. Load MTZ File Click! Joana Pereira Arp. Navigator Tutorials

1. Load MTZ File Change as you wish Joana Pereira Arp. Navigator Tutorials

1. Loading MTZ File Click! … Or choose a color! Joana Pereira Arp. Navigator Tutorials

1. Load MTZ File Click! Joana Pereira Arp. Navigator Tutorials

1. Load MTZ File Extend map: E + left button + mouse moved Joana Pereira Arp. Navigator Tutorials

2. Build Helices (Only) or Skeletons Right Click! Be sure this is visible and selected! Joana Pereira Arp. Navigator Tutorials

2. Build Helices (Only) or Skeletons Choose one Joana Pereira Arp. Navigator Tutorials

1. 1. Build Helices (Only) Click! Joana Pereira Arp. Navigator Tutorials

1. 1. Build Helices (Only) Click! Joana Pereira Arp. Navigator Tutorials

1. 2. Build Skeletons Click! Joana Pereira Arp. Navigator Tutorials

1. 2. Build Skeletons Click! Joana Pereira Arp. Navigator Tutorials

For any questions… The Developers Contact us anytime! Victor Lamzin Philipp Heuser Ioan Vancea Ciaran Carolan Tim Wiegels Joana Pereira We are here! Or just visit our website! http: //www. embl-hamburg. de/ARP/ User guide Frequently asked questions Tutorials Joana Pereira EMBL @ Desy Hamburg Arp. Navigator Tutorials