Volumes used by crysol
Posted: 2017.04.27 14:22
When calculating a scattering profile using crysol a number of radii and volumes are used and reported. I'm trying to figure out what they are and how they are used in the calculation of the scattering profile.
here I did a test with a random PDB file:
Crysol reports a "dry volume", is that simply the volume of the individual atoms and atomic groups (Ie the sum of Vj in the original crysol paper)? And when fitting, is this value influenced by the choice of Ra?
When fitting to an experimental curve, crysol fits a volume (in addition to Ra), is this what is displayed as "Excluded Volume" in the above?
Finally there is also something called "Displaced volume" which in the current case is the same as the "Excluded volume", but it is not clear for me what this volume is or how its used (if it is used at all).
I suspect that the reported "Excluded volume" is used to calculate the scattering profile of the excluded solvent (see viewtopic.php?f=11&t=2214):
I(s) = <|Aa(s) - (V/V0)*p0*Ac(s)+dp*Ab(s)|^2>omega
where V is the "Excluded volume" (which may be adjusted to fit the data). If i'm correct, Is the "Dry volume" then V0?
When calculating (not fitting to data) a scattering curve, is the parameter Ra set to the average atomic radius?
I hope you can help shed some light on these parameters.
here I did a test with a random PDB file:
Code: Select all
C R Y S O L Version 2.8.3 -- 04/10/12
-- Program started at 26-Apr-2017 09:37:34--
-------- Real space resolution and grid --------
Maximum order of harmonics ............................ : 15
Order of Fibonacci grid ............................... : 17
Total number of directions ............................ : 2585
------------ Reciprocal space grid -------------
in s = 4*pi*sin(theta)/lambda [1/angstrom]
Maximum scattering angle .............................. : 0.5000
Number of angular points .............................. : 51
--- Structural parameters (sizes in angstroms) ---
PDB file name .......................................... : linoleic.pdb
Number of atoms read .................................. : 52
Geometric Center: 8.037 0.749 7.158
Number of carbons read ................................ : 18
Number of oxygens read ................................ : 2
Number of hydrogen atoms read ......................... : 32
Center of the excess electron density: 29.071 2.364 -3.368
Electron Rg : 6.408 Envelope Rg : 6.730
Shape Rg : 6.260 Envelope volume : 603.1
Shell volume : 1328. Envelope surface : 259.6
Shell Rg : 8.503 Envelope radius : 11.29
Shell width : 3.000 Envelope diameter : 22.12
Molecular Weight: 280.4 Dry volume : 339.9
Displaced volume: 478.3 Average atomic rad.: 1.300
-- No data fitting, parameters entered manually --
Solvent density ........................................ : 0.3340
Contrast of the solvation shell ........................ : 3.000e-2
Average atomic radius .................................. : 1.300
Excluded Volume ........................................ : 478.3
Average atomic volume .................................. : 9.198
Radius of gyration from atomic structure ............... : 8.988
Average electron density ............................... : 0.3261
---------------- Output files ------------------
Intensities saved to file linoleic00.int
Net amplitudes saved to file linoleic00.alm
C R Y S O L Version 2.8.3 -- 04/10/12 ---- terminated at 26-Apr-2017 09:37:34--
Crysol reports a "dry volume", is that simply the volume of the individual atoms and atomic groups (Ie the sum of Vj in the original crysol paper)? And when fitting, is this value influenced by the choice of Ra?
When fitting to an experimental curve, crysol fits a volume (in addition to Ra), is this what is displayed as "Excluded Volume" in the above?
Finally there is also something called "Displaced volume" which in the current case is the same as the "Excluded volume", but it is not clear for me what this volume is or how its used (if it is used at all).
I suspect that the reported "Excluded volume" is used to calculate the scattering profile of the excluded solvent (see viewtopic.php?f=11&t=2214):
I(s) = <|Aa(s) - (V/V0)*p0*Ac(s)+dp*Ab(s)|^2>omega
where V is the "Excluded volume" (which may be adjusted to fit the data). If i'm correct, Is the "Dry volume" then V0?
When calculating (not fitting to data) a scattering curve, is the parameter Ra set to the average atomic radius?
I hope you can help shed some light on these parameters.
