TutorialMontevideo2015

There is a very good set of tutorials available from the Erice 2014 workshop. You can follow one of those or work on your own data/problem if you want. Remember that you have a BUSTER reference card to get help - or search this Wiki (box on the upper left).

In the above section the commands you should type into a terminal are shown in green - as in

ls -ltra

The material here is specifically tuned to the length and setup of this workshop.

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A good example of using BUSTER (and associated tools) would be 1PMQ.

1. Setup

Create a fresh directory via

mkdir ~/BUSTER-tutorial

and go there with

cd ~/BUSTER-tutorial

You can get the required data files via

fetch_PDB 1PMQ

or save the following files:

• 1pmq.pdb
• 1pmq.mtz

You will also need a restraints dictionary for residue 880 - either from http://grade.globalphasing.org or save the file

• 880.grade_PDB_ligand.cif

2. Running BUSTER

To just compute a map you would use the command (check your BUSTER reference card)

refine -p 1pmq.pdb -m 1pmq.mtz -l 880.grade_PDB_ligand.cif -M MapOnly -d MapOnly | tee MapOnly.lis

and then visualise the results using

cd MapOnly
visualise-geometry-coot

Alternatively, you could run a full series of BUSTER refinements that are rather typical for getting started with BUSTER on a structure without NCS:

refine -p 1pmq.pdb -m 1pmq.mtz -RB  -l 880.grade_PDB_ligand.cif -d 01 | tee 01.lis
refine -p 01/refine.pdb -m 1pmq.mtz -M TLSbasic  -l 880.grade_PDB_ligand.cif -d 02 | tee 02.lis
refine -p 02/refine.pdb -m 1pmq.mtz -M TLSalternate -TLS -M WaterUpdatePkmaps  -l 880.grade_PDB_ligand.cif -d 03 | tee 03.lis
 

The above is just an example of BUSTER refinements when starting from a deposited PDB structure. Different starting points (poor initial model, domains missing, low-resolution etc) might need a slightly different approach. See the extensive material on this wiki for some pointers ...

3. Visualisation of results

Again, visualisation would be best done via

cd 03
visualise-geometry-coot

For details about this tool please see here. You will be presented with a box showing you so-called 'unhappy' atoms: thse are atoms you can work through to see if there is something that needs manual attention.

Also, all other Coot tools can be used to analyse your structure - which would show you a potential issue at residue A45:

After correcting this, you can start a quick BUSTER job using the "BUSTER" button at the top right

After pointig to the correct MTZ file (1pmq.mtz) you can just compute a BUSTER map or do a short refinement:

After those initial steps, any subsequent BUSTER refinement would use commands like

refine -p 03/refine-coot-0.pdb -m 1pmq.mtz -M TLSalternate -TLS -l 880.grade_PDB_ligand.cif -d 04 | tee 04.lis

Details:

• use the latest PDB file from manual adjustment in Coot
• no automatic water-update (since solvent structure already fairly complete and manual work required to get to the 100% level)
• output of each subsequent run goes into separate subdirectory and we are saving standard output as well (come up withe some meaningful system - here we're using an increasing 2-digit number)

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If you want to work with your own structure:

• look at BUSTER reference card

• look at material on this wiki

• get ligand restraint dictionaries from http://grade.globalphasing.org/

• if you have NCS:
• start with -autoncs_noprune -sim_swap_equiv
• then switch to -autoncs

• if using TLS:
• start with -M TLSbasic
• then switch to -M TLSalternate -TLS

• for occupancy refinement, have a look at pdb2occ tool and some tutorial

• difference Fourier maps are described here