Quick Start IV. Fast and Better Structure Solution, Faster on
Clusters
{0}. i) Log on
to the cluster using: ssh X
username@idc11
ii) Go to the directory with your *.sca data
file(s).
iii) sgxpro
* Try login as staff and copy/scp your .sca file there, if your account on the cluster has problems.
* Use sgxjobcheck help to see how to terminate multiple jobs when needed.
{1}. Solving
Structure by SAD or MAD and SAD
B
Warning: Be realistic when set resolutions
here! If the high resolution data
doesnt have signal at all (all noise, processed too aggressively!),
SOLVE/RESOLVE may fail and run forever without solution. If you see a job keeps running while
others having long finished, kill it!, SGXPro will
still get the solution from others that finish normally. E G F D C A
A. Click on Novel Structure Solution button.
B. Browse a .sca file with unit cell information (Make sure the space group is right).
C. i) Browse the sequence file of FASTA format (You may also give the number of
residues and click on Create an all ALA Seq to generate an all-ALA sequence,
which may build better main chain.);
ii) Click on Estimate Possible Solvent Contents; iii) Select a solvent content.
D. Select a phasing method SAD or MAD.
E. Browse the .sca file(s) (output from HKL2000 with anomalous on).
Give wavelength (A/EV), number of sites, heavy-atom type (HA), Fp, Fpp.
For MAD, you may load as many as 4, as few as 2 data sets.
F. Click on Save button.
G. Click on Run button.
Results Summary (you may open it with SGXPRO built-in editor or vi etc.):
1). *.shelxd.log (best CC all/weak of above 30/above 10 is a good sign).
2).
Structure Solution
Upon finishing, top five solutions from the algorithm and parameter space searching
are saved in files:
zzsgxSol_#.pdb (model from RESOLVE auto_tracing),
zzsgxSol_#.mtz (phased data in RESOLVE MTZ format),
zzsgxSol_#.phs (phased data in PHASES format),
zzsgxSol_#_ha.pdb (heavy atom sites).
The zzsgxSol_tracing.summary contains the summary of auto-tracing results.
3). Check density
SGXPRO will automatically choose and use COOT to display the model & density
map of the best solution (from the COOTs Column Label Assignment GUI page,
select Use Weight? and click on OK, see below.). You may check the model &
density map of any other solution by using command:
coot --pdb zzsgxSol_#.pdb --data zzsgxSol_#.mtz.
4). XtalView: The zzsgxSol_1.phs file contains the phase data, which is in
PHASES format that together with model in the zzsgxSol_1.pdb file can be
directly read into the application Xfit of XTALVIEW (SGXPRO
-> Density
Fitting -> XtalView). You need to create a Project and setup the
information before starting Xfit.
{2}. Sequence-Homologue Structural Template Searching
& Molecular Replacement
G B E F D C A 
A. Click on Molecular Replacement.
B. Browse your sequence file in FASTA format, which will connect and search the
NCBI database. If you have your own model, skip this step and go to step C to
Browse (button pointed by the blue arrow) in your own model.
C. From the result list, select a
structural template. Then, click on Download
PDB
File. The selected entry will be downloaded from PDB. You may also Browse
(button pointed by the blue arrow) in your own model.
D. For each PDB file, fill in PDB ID (any 4-letter unique string if
not exist), Sequence
Identity (fractional), Molecular Weight (in KD) and Number of Copies of this
model in one AU. Then, click Add button to add the model.
* Each model added will be treated as a substructure in the AU.
E. Browse your native data in .sca format (e.g. HKL2000 with anomalous off).
Warning: Each PDB file may contains multiple molecules. Before click on Save,
you have to manually edit each PDB file to make sure it contains only the
template structure(s) that you want!!!
F. Click on Save button.
G. Click on Run button. The results are summarized in zzsgxSol_mr.summary.
Ref: Fu, Z.-Q., Rose, J. & Wang, B.-C. (2005): Acta Cryst. D61:951-959.