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