Content:
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:
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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:
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 |
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 |
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 |
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 |
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 |
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 |