DaRa/Crysol

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
Post Reply
Message
Author
Ashar85
Guest
Posts: 2
Joined: 2015.10.02 14:14

DaRa/Crysol

#1 Post by Ashar85 » 2015.10.02 14:44

Hey there,

This may sound stupid but please bear with me.

In the "Prototype of a database for rapid protein classification based on solution scattering data" publication http://www.embl-hamburg.de/biosaxs/repr ... c_2003.pdf dated 2003, Figure 1 shows a generic SAXS profile running till 10 (s, nm). All subsequent figures make use of Crysol and profiles run up till 1.0 (s, nm). Crysol which I am guessing makes the back bone of DaRa lists on its manual page the flag -sm set as default to 0.5 Å-1 and that it can go max till 1.0 Å-1.

Questions:

just to make sure that I have gotten this correctly -- if I set the -sm flag in crysol (command line) to "1" -- it would mean that the resulting profile will go till 10 (s, nm). Right ? If the above is true -- the red section for the same (4 - 9 nm) in figure 1 would not hold true --- or would it? I am sure nm^-1 and nm are not the same units and only one of the two can be true (or maybe I am just not thinking right???).

Some feedback on this would be appreciated,

User avatar
AL
Administrator
Posts: 642
Joined: 2007.08.03 18:55
Location: EMBL Hamburg, Germany
Contact:

DARA 2003 paper erratum

#2 Post by AL » 2015.10.05 22:25

Ashar85 wrote:Figure 1 shows a generic SAXS profile running till 10 (s, nm). All subsequent figures make use of Crysol and profiles run up till 1.0 (s, nm).
Obviously there is a mistake: Figures 3, 4, 5 and 6 should be labelled "s, Å-1". Figure 1 should be labelled "s, nm-1".
Ashar85 wrote:if I set the -sm flag in crysol (command line) to "1" -- it would mean that the resulting profile will go till 10 (s, nm). Right ?
"crysol -sm 1" means "compute the scattering up to 1 Å-1", i.e. up to 10 nm-1.
I hope it is clear now.

Ashar85
Guest
Posts: 2
Joined: 2015.10.02 14:14

Re: DaRa/Crysol

#3 Post by Ashar85 » 2015.10.05 22:39

Yeah -- thanks :)
It was clear before as well from the other literature i was going through -- the figure just threw me off.

Thanks for seconding it though :)

Best,
/A

Post Reply