coral and hexameric particle

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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gia75
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coral and hexameric particle

#1 Post by gia75 » 2014.12.17 13:24

Hi All,

i have an hexameric particle (symmetry P32, dimer of trimer, or trimer of dimer...) with known crystal structure of the hexamer.
I have missing n-term (6x) and moving loops so i would like to use CORAL to model the particle.
i have already tried CORAL in P1 by fixing the 6 chains and I would like to optimize the fit (best CHI is 2.5)

Question1:
is it possible to use contact conditions (or distances) when imposing P32 symmetry ?

Question2:
why do I get much higher CHI when I use CRSYOL to fit the CORAL model into my data ?

Thank you in advance,

GIA

Egon
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Re: coral and hexameric particle

#2 Post by Egon » 2015.01.16 12:45

Hi All,


I have the same problem concerning the huge difference between the Chi values CORAL gives me and the Chi values I get when I take these models to Crysol. The best CORAL outputs are around Chi values of 2,5. When I run crysol with this I get a Chi value of 20.


Thanks a lot,


Egon

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AL
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P32 in CORAL

#3 Post by AL » 2015.01.19 15:53

gia75 wrote:Question1:
is it possible to use contact conditions (or distances) when imposing P32 symmetry ?
Yes. CRYSOL online does not support contact conditions yet, you need to run the command-line version.


I guess what you really want is to keep the known crystal structure of the hexamer intact and to model the missing n-terms using the same P32 symmetry. You need to
  • align your hexamer model such that the P3 symmetry axis is aligned with the z axis and P2 symmetry axis is aligned with the y axis; make sure the model is in the centre of coordinates (0, 0, 0);
    leave one monomer, remove the other five monomers;
    run CORAL like this:
Overall symmetry: P32
Experimental data: your SAXS curve
Number of domains: 1
Domain 1: N-terminal: [number of missing residues] monomer.pdb fixed C-terminal -[/list]

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AL
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CRSYOL chi-square vs. CORAL chi-square

#4 Post by AL » 2015.01.19 16:25

gia75 wrote:Question2:
why do I get much higher CHI when I use CRSYOL to fit the CORAL model into my data ?
Egon wrote:The best CORAL outputs are around Chi values of 2,5. When I run crysol with this I get a Chi value of 20.
One could think of a number of reasons. E.g.
  • CORAL subtracted a large constant and in CRYSOL constant subtraction was not allowed;
    CRYSOL was used with a higher maximum order of harmonics and a higher order of the Fibonacci grid;
    the CORAL model is shifted from the centre of coordinates;
    different angular ranges were used;
    the angular units were wrong
and so on. It's hard to say why the chi-square values are different without seeing the model, the fits, the used options and the ATSAS version.
The way how CORAL is calculating the scattering from the current model is less precise compared to CRYSOL, i.e. the CRYSOL fit should be more trustworthy.

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