GASBORMX online: where are the volume fractions?

[Guðmundsdóttir]

I'm running GASBOR online in the 'Fit to oligomer-monomer mixture' mode. How do I find out what my oligomer-monomer ratio is?

[AL]

If you open the final model (.pdb) in a text editor you'll see something like

Code: Select all

 Volume fraction,oligomer ............................... : 0.6285
 Volume fraction, monomer ............................... : 0.3715

[sasandra]

In the current gasbormx version (atsas 3.2.1 r14885) in which output models are in .cif format, are the optimized volume fractions of monomer and oligomer still printed somewhere?
I was not able to find this information in any of the output files

[franke]

Hi sasandra. Indeed, this information got lost in the transition to mmCif format. It will be added back in the next release. My apologies

(if not too much trouble, you can install a 3.1.x version, there the information should still be provided. There should be no other significant differences in gasbormx besides the mmCif support in 3.2.1)

[AL]

I think you can fit your input data with OLIGOMER.
GASBORMX saves the scattering computed from the monomer and oligomer as 'xxx-monomer.dat' and 'xxx-oligomer.dat' (where xxx is the name of your "project").
Try:

ffmaker xxx-monomer.dat xxx-oligomer.dat --output=ff.dat
oligomer --ff ff.dat yourinputdata.dat --cst --un=2

(you need --un=2 only if your data are in nm^-1).
Make sure that 'yourinputdata.fit' is as good as 'gasbor.fir'.
The volume fractions will be written in 'oligomer.log'.