Hi.generally, we get the theoretical scattering curves from high-resolution structures by CROSOL,

but i was wondering How to generate the theoretical P(r) curve from pdb files? I know a example using CPPTRAJ in the AMBER 14 package to get the P(r) curve.

By the way, one more question, i get the advice to normalize the y-axs of the P(r) curves when a series of curves are compared from the forum,

But can we normaliz all the curves to a total area of 1? that'all, thanks in advance!

cheers,

WenKai Zhu

## How to generate the theoretical P(r) curve from pdb files?

### Re: How to generate the theoretical P(r) curve from pdb file

If you have ATSAS 2.7.2 the easiest would be to run CRYSOL and then use GNOM 5 on the predicted curve like this:zhuwenkai wrote:Hi.generally, we get the theoretical scattering curves from high-resolution structures by CROSOL,

but i was wondering How to generate the theoretical P(r) curve from pdb files?

Code: Select all

```
crysol model1.pdb -lm 30 -ns 256
gnom5 model100.int --rmax 100.0
```

If you want a better fit of the p(r) to your calculated curve - use smaller values of --alpha:

Code: Select all

`gnom5 model100.int --rmax 100.0 --alpha 0.01`

Since the area below the p(r) is equal to I(0)/4Π you may normalise all your curves by I(0) from AUTORG using DATOP DIV and then run GNOM. This way the p(r) functions should have the same area.zhuwenkai wrote:By the way, one more question, i get the advice to normalize the y-axs of the P(r) curves when a series of curves are compared from the forum,

But can we normaliz all the curves to a total area of 1?

### Re: How to generate the theoretical P(r) curve from pdb files?

Dear Zhuwenkai,

CaPP can calculate the theoretical p(r) directly from a PDB file (without any detour into reciprocal space):

https://github.com/Niels-Bohr-Institute ... ophys/CaPP

When comparing p(r) functions, I recommend normalising the maximum value to unity (i.e. divide by max{p(r)}), as this gives a good basis for visual comparison of the p(r) from proteins with different shapes.

CaPP can calculate the theoretical p(r) directly from a PDB file (without any detour into reciprocal space):

https://github.com/Niels-Bohr-Institute ... ophys/CaPP

When comparing p(r) functions, I recommend normalising the maximum value to unity (i.e. divide by max{p(r)}), as this gives a good basis for visual comparison of the p(r) from proteins with different shapes.

### Re: How to generate the theoretical P(r) curve from pdb files?

OBS

CaPP is now updated with several bug-fixes, and possibility for deuteration (SANS), and possibility for inclusion of explicit H and D. So please use the latest version:

https://github.com/Niels-Bohr-Institute ... ophys/CaPP

- and it's 100% open source

CaPP is now updated with several bug-fixes, and possibility for deuteration (SANS), and possibility for inclusion of explicit H and D. So please use the latest version:

https://github.com/Niels-Bohr-Institute ... ophys/CaPP

- and it's 100% open source