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Excluded volume fit in CRYSOL

Posted: 2013.12.18 21:43
by dggreene
Hi

In the CRYSOL paper it lists only 2 adjustable parameters in the fit, the density of the hydration layer and the effective atomic radius, r0. However, there are 3 adjustable parameters in the software, the density of the hydration layer, the optimal atomic radius,Ra, and the excluded volume. The paper states r0 is "a variable parameter that can be used to change the displaced volume per atomic group and thus to adjust the total excluded volume".

My questions are:

1). Why are there 3 adjustable parameters in the code while the paper only has 2. Specifically, why is excluded volume an adjustable parameter when the paper clearly states that excluded volume is a function of r0?
2). Does the parameter "Ra" correspond to r0?

Thanks

Re: Excluded volume fit in CRYSOL

Posted: 2014.01.02 22:26
by SaxsMax
1. The original Crysol paper has been published in 1995.
There were a number of changes since then.
Particularly, the total excluded volume has been decoupled
from the variation of the average atomic group radius
since Crysol v. 2.3 (in year 2001).
2. Yes, Ra is the same as r0 in the paper

Re: Excluded volume fit in CRYSOL

Posted: 2014.01.06 16:47
by dggreene
Ok.

How does the excluded volume enter into the calculation now that it is decoupled?

Do you have more up to date documentation about the specifics of the calculation?

Thanks

Re: Excluded volume fit in CRYSOL

Posted: 2014.01.06 17:48
by SaxsMax
Now a coefficient (V/V0) is used for the excluded volume amplitude.
V is adjusted within 0.925*V0 to 1.075*V0 where V0 is the volume computed by default.
In a way it is equivalent to the adjustment of the bulk solvent density.

You could have a look at the SASdoc manual delivered with Atsas package
or online at
http://www.embl-hamburg.de/biosaxs/manuals/crysol.html

Re: Excluded volume fit in CRYSOL

Posted: 2014.01.06 18:30
by dggreene
Does eqn 1 from the paper then become,
I(s) = <|Aa(s)+ (V/V0)*p0*Ac(s)+dp*Ab(s)|^2>omega ?

Also, is V0 part of the output log file?

Thanks

Re: Excluded volume fit in CRYSOL

Posted: 2014.01.06 18:54
by SaxsMax
Does eqn 1 from the paper then become,
I(s) = <|Aa(s)+ (V/V0)*p0*Ac(s)+dp*Ab(s)|^2>omega ?
Yes
Also, is V0 part of the output log file?
It is written in the log file in the prediction mode (i.e. w/o fitting) as "Excluded Volume"
In the fitting mode it is present indirectly as the limits "ExVol(Min/max)"
corresponding to 0.925*V0 and 1.075*V0, respectively