Frequently Asked Questions:

Questions:

1. Is sastbx and the online service free?
2. What is the file format for saxs profile?
3. If I have saxs profile and a PDB model, can I compare the PDB model to the model from shapeup?
4. The PDB model is not displayed in the Jmol plugin, what can I do?
5. The Jmol applet is there, but no model is loaded?
6. Can you refine a PDB model, so that it agrees with data?
7. What do you mean by 'clean' saxs data?
n. Other Questions? Any place for discussion, or posting questions?

Answers:

1. Is sastbx and the online server free?
Yes! See more at sastbx home page: http://sastbx.als.lbl.gov.

2. What is the file format for saxs profile?
Standard. A text file with three column: q, i, sigma. For Example: # Comments can be put after '#' # q i s 0.01 100.0 4.2 0.02 98.0 4.0 ...

3. If I have saxs profile and a PDB model, can I compare the PDB model to the model from shapeup?
Yes. Just supply both file to the webserver, and the models will be superposed, and a corrleation coefficient score will be computed.

4. The PDB model is not displayed in the Jmol plugin, what can I do?
Opps.. But dont worry, the Models are there! Jmol only render standard PDB file to Cartoon. You can try to change a representation of the PDB model. For example: Right click in the Jmol Applet, and go to surfaceMenu, then click surfDots. You will see the dot representation of your model.

5. The Jmol applet is there, but no model is loaded?
We apologize for that. At the moment, we are not sure yet, but if you refresh the page, it may just load. One possible explanation is that the network is slow to load models in time for nice display. If that does not help, why not download the files and use your favorite viewer to look at the models: They are in standard CCP4 format (We can make CNS/Xplor format files, too).

6. Can you refine a PDB model, so that it agrees with data?
Yes. We have iterative normal mode perturbation method to refine the models. Unfortunately, it is not online yet. You can use the stand alone version.

7. What do you mean by 'clean' saxs data?
The word 'clean' is defined as 'no obvious fluctuation'. The saxs data at low_q is critical for getting correct 'radius of gyration' and will affect the subsequent analysis. Our suggestion is to cut 'suspecious' low q data, such that the Guinier region look nice.

n. Other Questions? Any place for discussion, or posting questions?
Check out Google Group on SAS software. Or, Send to me haiguang.liu@gmail.com.