TutorialRapiData2015

20150505: Work in progress (throughout the course)

Content:

• Introduction
• Tutorial schedule
• autoPROC
• Setup
• Tutorials
• Setting up using Coot

---

Introduction

Here we will collect some information regarding use of our software (during tutorials or when using it on your own) that is particular to the setup during RapiData 2015.

We will try and keep this page here up-to-date as we get settled in during the course.

---

Tutorial schedule

We are giving tutorials on autoPROC (data processing - see here) and SHARP/autoSHARP (experimental phasing and structure solution) in Building 137E 2nd floor, room 226 - see this map.

Please use the sign-up sheets outside the lecture hall so that we can plan the tutorials. But otherwise: just find us and talk to us at any time during the course (coffee/lunch breaks are a good opportunity) - especially if you are interested in discussing data collection strategies for experimental phasing before doing the actual experiment!

---

Setup

There are different ways of running autoSHARP:

• the most complete interface to SHARP/autoSHARP is available at the SHARP server http://pxproc00:8080/ (username "rapidata" with password "RapidSharp").

• within the CCP4i there is an autoSHARP task in

      Experimental Phasing
        --> Automated Search & Phasing
              --> autoSHARP

• if you can type run_autoSHARP.sh -h in a terminal (and it comes back with the help message), then everything should be setup correctly for using the command-line interface to autoSHARP. You might want to have a printout of the autosharp_reference_card.pdf (file not found) handy to help with usage.

---

Tutorials

Most of the information here should be enough to download some example data and start using autoSHARP through any of the above interfaces.

Remember that you can download the provided example files

by moving the pointer over a link and clicking the right mouse button

Then select "Save link as ..."

and save it in the ~/Downloads folder:

You can then upload those files to the SHARP server from the main Control panel via the "upload files" link

and "Browse" to the ~/Downloads folder

Once the relevant files have been selected, you "Submit" it

---

Setting up using Coot

In order to view maps/models, the default interface provides a single-button solutions to start Coot:

It will initially ask what to use

You need to browse to /home/sw/sharp/20150504/bin

select helpers.x-coot

and click "Open". If everything works for you after this, you could also check the "Do this automatically for files like this from now on"