Hello,
Apologies for the naive question, I hope this has not been asked already. I have successfully installed IMP and gone through the multifit tutorial with 3sfd.
I am in the process of implementing multifit for initial fitting of our own EM density with proteomics data. However, I have a question regarding the proteomics restraint file. in the example file:
|proteins| |3sfdA|1|613|nn|nn| |3sfdB|1|239|nn|nn| |3sfdC|1|138|nn|nn| |3sfdD|1|102|nn|nn| |interactions| |residue-xlink| |1|3sfdB|23|3sfdA|456|30| |1|3sfdB|241|3sfdC|112|30| |1|3sfdB|205|3sfdD|37|30| |1|3sfdB|177|3sfdD|99|30| |1|3sfdC|95|3sfdD|132|30| |1|3sfdC|9|3sfdD|37|30| |1|3sfdC|78|3sfdD|128|30| |ev-pairs| |3sfdB|3sfdA| |3sfdB|3sfdC| |3sfdC|3sfdD|
It is unclear to me what each of the fields means in the "proteins" section and the meaning of the first field in the "residue-xlink" section. I assume "30" is the maximum distacnce from experimental data? What potential is used for these restraints?
Many thanks in advance,
Andrea
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
participants (2)
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Andrea Graziadei -
Ben Webb