Search found 347 matches

by SaxsMax
2017.06.19 12:47
Forum: Working with Models
Topic: Obtaining Profiles With Explicit Waters
Replies: 2
Views: 4524

Re: Obtaining Profiles With Explicit Waters

One can change "WAT" to "H2O" for example and then use "-eh" and "-dro=0" keywords in the command line
by SaxsMax
2017.05.31 13:49
Forum: Working with Models
Topic: Volumes used by crysol
Replies: 5
Views: 5522

Re: Volumes used by crysol

Please note that the formfactors are still computed from Gaussian spheres, not solid spheres
by SaxsMax
2017.05.31 13:43
Forum: Working with Models
Topic: Volumes used by crysol
Replies: 5
Views: 5522

Re: Volumes used by crysol

Fraser et al. (1978) lists observed volumes for just four atoms.
The present version of Crysol supports 108 atom and atomic groups (e.g. CH)
whose Wan-der-Waals volumes seem to work well.
by SaxsMax
2017.05.31 12:18
Forum: Working with Models
Topic: Atomic form factors and incoherent scattering in Cryson
Replies: 1
Views: 3870

Re: Atomic form factors and incoherent scattering in Cryson

In Cryson the form factors for individual atoms are constants equal to the corresponding scattering lengths
but for the atomic groups (like CH) the formfactors are computed using the Debye formula and therefore depend on s.

Incoherent scattering is not taken into account in prediction mode.
by SaxsMax
2017.05.10 11:45
Forum: Working with Models
Topic: Volumes used by crysol
Replies: 5
Views: 5522

Re: Volumes used by crysol

Dry volume is simply computed from the molecular weight as V=1.21*MW where MW is in Dalton and V is in A^3. Displaced volume is the sum of the Van-der-Waals volumes of individual atomic groups, (i.e. it serves as V0 in formula). Excluded volume is the adjusted value (V in the formula, in prediction ...
by SaxsMax
2017.03.14 11:31
Forum: Rigid Body Modelling
Topic: Coral Restrains chain ID problem
Replies: 9
Views: 7134

Re: Coral Restrains chain ID problem

Hi,

Internally Coral puts all the input proteins into one "superchain",
therefore the reported numbering is different from the dist.cnd.
Have you checked that the conbdition is fulfilled in the resulting model?
by SaxsMax
2017.02.02 13:24
Forum: Rigid Body Modelling
Topic: Slit smearing in SASREF and BUNCH
Replies: 4
Views: 6497

Re: Slit smearing in SASREF and BUNCH

The smearing is done according to the equation (9.26) from Feigin&Svergun book, page 295 with W(t)=2*Smax (i.e. constant) corresponding to an infinite slit.
by SaxsMax
2017.01.13 18:02
Forum: Working with Models
Topic: Using Crysol for non-biological systems
Replies: 2
Views: 4356

Re: Using Crysol for non-biological systems

If PDB file contains standard atoms, one can use Crysol in the same way as for biological molecules
by SaxsMax
2016.12.20 16:27
Forum: Working with Models
Topic: Reliability of Crysol theoretical curves
Replies: 5
Views: 5428

Re: Reliability of Crysol theoretical curves

The smoothing of the experimental pattern could be either due to polydispersity (which you beleive is not the case) or due to some flexibility in the positions of the monomers within the 24mer. Possibly, you could use the experimental profiles of the 100% 24mer and of the 100% dimer to deconvolute t...
by SaxsMax
2016.11.24 12:36
Forum: Ab Initio Shape Determination
Topic: Strange outputs from MONSA
Replies: 2
Views: 4287

Re: Strange outputs from MONSA

Seemingly, something is completely wrong with the modelling,
as the program made just two simulated annealing steps
instead of a hundred. Therefore the solution looks like a ball with mixed beads
by SaxsMax
2016.11.04 13:48
Forum: Rigid Body Modelling
Topic: DNA and SASREF
Replies: 2
Views: 4083

Re: DNA and SASREF

As for DNA, its sequence does not change in Sasref, but both strands get the same chain id
by SaxsMax
2016.11.04 13:22
Forum: Rigid Body Modelling
Topic: DNA and SASREF
Replies: 2
Views: 4083

Re: DNA and SASREF

Online Sasref has actually the problem with CZ38_ZF8_ZN_KE-TG.pdb file which has a line "HETATM 248 ZN ZN _ 1 3.166 1.522 -4.762 1.00 0.55 ZN" The line contains a special tab character and cannot be read. Please replace it with "HETATM 248 ZN ZN _ 1 3.166 1.522 -4.762 1.00 0.55 ZN" I have edited thi...
by SaxsMax
2016.03.22 13:41
Forum: Working with Models
Topic: CRYSOL fitting error
Replies: 1
Views: 1977

Re: CRYSOL fitting error

Weifeng, thank you for the report.
The issue is caused by the second but last point with zero intensity and error.
3.893170e-01 0.000000e+00 0.000000e+00
We should correct this in the next 2.7.2 release.
For the moment you could simply remove this point from the data file
by SaxsMax
2015.07.21 18:55
Forum: Working with Models
Topic: Crysol can not find Experimental Rg value from the data file
Replies: 2
Views: 2406

Re: Crysol can not find Experimental Rg value from the data

Did you cut the bad data points at the beginning that do not behave according to the Guinier law?
by SaxsMax
2015.07.03 13:42
Forum: Working with Models
Topic: Crysol atsas 2.6
Replies: 4
Views: 2878

Re: Crysol atsas 2.6

OK, I might have got the idea whats going on.
You colleague might have computed the fit using the graphical (qw) version of Crysol
which was updated later than the 2.6 release was made.
This issue in qw should be fixed in the 2.6.1 which should be out soon