Re: [IMP-users] multifit proteomics file

[Ben Webb <>]

On 12/5/18 7:06 AM, Andrea Graziadei wrote:
> It is unclear to me what each of the fields means in the "proteins" section

The first three fields, from left to right, are:
  - protein name
  - first residue index (usually 1)
  - last residue index
The remaining fields are used to specify file names of the protein, 
surface, and reference, but I think are generally unused.

> and the meaning of the first field in the "residue-xlink" section.

If set to 1, the interaction is also used as a filter in the 
construction of the junction tree, which is probably what you want.

> I assume "30" is the maximum distacnce from experimental data?
> What potential is used for these restraints?

As far as I can tell from the code, the distance isn't used directly, 
but crosslink data just ensures that the given subunits are found in 
proximity via a connectivity restraint.

BTW, MultiFit hasn't been under active development for some time. For 
any more complex integrative modeling there are a number of more recent 
solutions in IMP - the PMI module is a good place to start.

	Ben
--
                      https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle