UNDER CONSTRUCTION (throughout the workshop)

Content

Introduction

These pages are intended as a resource for the tutorials of our software at the International workshop, Joint CeBEM-CCP4 initiative, April 9th-17th, 2013, Institut Pasteur Montevideo, Uruguay .

Much more introductory material is available for each program:

Local setup

All programs should be configured and setup correctly. You can test this by running 

% process -h
% refine -h

and by pointing your browser (firefox) to http://localhost:8080/ (username/password = pasteur/sharp). If the SHARP server isn't running - try (re)starting it with 

% $BDG_home/start.sh

If this doesn't work - please contact the tutors.

Helper applications

When looking at the results of the program (through your browser), there are links to graphical information like plots, PDB files, electron-density maps etc.

helpers_01.png

(When running autoSHARP through the CCP4i interface graphical results are presented as simple links instead!)

Those will be visualised through external applications like Coot - in the same way as you might look at PDF files with Acrobat when browsing the internet. Anyway, in order to get this going a little bit of work is required by the user the first time a specific type of result is encountered. You will see a pop-up appearing that looks similar to this:

helpers_02.png

We now need to tell it to use a specific helpers script that comes as part of our software installation - so the place where this helper script is residing on your computer might vary. It is a good idea to type (in a terminal): 

% ls $BDG_home/bin/helpers.x-*

which will show the various helper script (for different type of files/results). Using the "Open with" item we can either browse to pick the right helper script or write the full path directly:

helpers_03.png

Finally, we want to use the same method every time - which will mean the correct helper application will pop up automaticaly the next time:

helpers_04.png

Sometimes it might become necessary to redo the steps above - but the browser doesn't ask the user to pick the correct helper application anymore. Then it becomes necessary to reset the handling within the browser, eg. in Firefox using the "Edit" ...

helpers_05.png

... "Preferences" ...

helpers_06.png

... "Applications":

helpers_07.png

After changing the action for the "3D plots in Coot" from "Use helpers.x-coot" back to the "Always ask", the above sequence of getting asked, browsing and selecting the appropriate helper application script can be done again.

1o22

This should be a reasonably fast run through all stages of data-processing (5 min), structure solution (15 min) and refinement (15 min) using a single example dataset (timings are for an i7-2720QM laptop with 8Gb of memory).

We're going to use the data for 1O22 from the JCSG. It is

Hopefully, you managed to follow the autoPROC tutorial for processing the peak dataset (in which case you will have a file aimless.sca in the output directory). Alternatively, we also provide a reflection file below.

To get data into the program, start on the so-called "SHARP Control Panel" and the "Upload files" link:

SHARPUpload_01.png

Then "Browse" to the file (MTZ, SCA, PIR, PDB etc - eg 1o22.pir and 1o22_peak.sca):

SHARPUpload_02.png

Finally, hit the "Submit" button

SHARPUpload_03.png

Remember: if you get lost you can always go back to the "SHARP Control Panel" using the URL http://localhost:8080/

SHARPUpload_04.png

SHARP/autoSHARP (experimental phasing and structure solution)

Please also have a look at the examples and tutorials on the SHARP/autoSHARP wiki.

We can use the data just processed for solving the structure with autoSHARP (run through the Sushi http-interface). To start autoSHARP from the main "SHARP Control Panel", Start it afresh (ie. select "None" from the pull-down menu to the right:

autoSHARP_01_crop.png

In order to have a quick run through the software during this tutorial, we will change the defaul mode to "fast":

autoSHARP_02_crop.png

In general, it is better to leave it at the default (accurate) to be more confident that a shortcut to achieve faster execution doesn't hinder successful structure solution.

Remember what we know about the project:

Filling in this information will look like this: first we need to give our job a meaningful and short identifier (without spaces or any "funny" characters). We also want to select the sequence file 1o22.pir (containing sequence of a monomer):

autoSHARP_04_crop.png

The remainder is relatively easy too - make sure you give the number of expected sites per monomer too:

autoSHARP_05_crop.png

the final step - just submit the calculation

autoSHARP_06_crop.png

and continue to the main autoSHARP logfile:

autoSHARP_07_crop.png

Rember that you need to "reload" that page from time to time:

autoSHARP_08_crop.png

After about 10 minutes we should have

This model has 145 out of 170 residues buit with R/Rfree = 0.219/0.259 : autoSHARP_02.png Remember, the deposited model contains 149 residues - so we are basically finishing with a complete model.

own data

This is the fun bit - working with your own data. You should be able to get very far all on your own. But if there are any questions: just let us know - also during coffee breaks etc!

SHARP/autoSHARP (experimental phasing and structure solution)

Make sure you have your sequence in a simple ASCII file and that you have a very good idea about your fluorescence scan (for anomalous signal data). You can get data files into the SHARP server (the httpd) through the 'Upload' mechanism on the main page.

There is an alternative (but less well tested and supported) interface to autoSHARP within CCP4i:

autoSHARP_CCP4i_01.png

which leads you to

autoSHARP_CCP4i_02.png

Original page: April 2013, Clemens Vonrhein