Content:


Introduction

All our software should be installed and directly useable for you. You can use autoSHARP in several ways: through the command-line interface, the normal httpd-based interface (http://localhost:8081/) or the CCP4i interface:

autoSHARP_ccp4i.png

Pick the interface you feel most confident with: the httpd-based and the command-line interface are possibly the easiest when it comes to viewing intermediate and final results (maps and models). But if you are more familiar with the CCP4i interface, this might be the easiest way for getting to know autoSHARP. The new command-line interface will create so-called Coot scripts that can be used eg as

% coot --script 07_coot.scm

Content:


Example data

SAD

This is reasonably fast.

PDB 1O22 (see also here)
Sequence details
Sequence (monomer) file 1o22.pir
Wavelength 0.9778 (Se-MET, peak)
f',f" = -7 5
1o22_peak.sca

MAD

This is a very fast example to run.

PDB 3ISY (see also here)
Sequence details
Sequence (monomer) file 3isy.pir
Wavelength 1 0.97934 (Se-MET, infl)
f',f" = -11 3.3
3isy_aimless_0.97934A.sca
Wavelength 2 0.91162 (Se-MET, hrem)
f',f" = -1.8 3.3
3isy_aimless_0.91162A.sca

SIRAS

An example that runs a bit longer.

PDB 1GXT
Sequence details
Sequence (monomer) file 1GXT.pir
Dataset 1 native
1GXT_nat.sca
Dataset 2 0.9997 A (Hg-derivative, 2 sites?)
f',f" = -16 10
1GXT_hg.sca

MIRAS

This is reasonably fast.

PDB 3ZFT
Sequence details
Sequence (monomer) file 3ZFT.pir
Dataset 1 native
3ZFT_nat.sca
Dataset 2 1.54179 A (Hg-derivative, 1 site?)
3ZFQ_Hg.sca
Dataset 2 1.54179 A (Ir-derivative, 2 sites?)
3ZFR_Ir.sca

Starting from partial model (SAD)

This can run for a longer time (depending on the computing hardware used).

PDB 3GET (see also here)
Sequence details
Sequence (monomer) file 3GET.pir
Starting, partial model 3FFH_ala_MR.pdb (poly-ALA of 3FFH, 28% sequence identity)
Wavelength 0.9789 (Se-MET, peak)
f',f" = -8 4
3GET.sca

Heavy-atom cluster (Ta6Br12)

Also an example that runs a bit longer.

PDB 4CV5
Sequence details
Sequence (monomer) file 4CV5.pir
Wavelength 1.25472 (Ta6Br12:Ta, peak)
4CV5.sca