- This topic has 3 replies, 2 voices, and was last updated 7 years, 8 months ago by Anonymous.
July 31, 2015 at 1:55 pm #2247Anonymous
Thank you for the informations in this forum which already helped me a lot. I have a question concerning constraints/restraints in RosettaCM. I want to predict the structure of a protein from which I know templates for two domains and several intramolecular crosslinks/distances between residues. As far as I understood only one template can be used for comparative modelling in the minirosetta application, so I chose RosettaCM for this chain.
How do I include the restraints in the best way?
I found the Mover ‘ConstraintSetMover’ and added it in my xml-file but I don’t really get how to do it in the best way, whether to use filters (does the filter ResidueDistance have something to do with it) or movers (eg AddConstraintsToCurrentConformationMover
?) and which one of them.
My restraints are atompairs for which I know the distance, I uploaded the xml-script.
Thank you a lot,
August 7, 2015 at 7:53 am #11121Anonymous
If someone could give me an example how to include the ConstraintSetMover in the XML-Script and whether it works together with the hybridize protocol that would help a lot as well. At the moment I don’t get measurable differences by adding the constraints in this way. Thank you!
August 11, 2015 at 7:24 pm #11136Anonymous
The way you have put the ConstraintSetMover should work.
Did you try scaling your constraint by large factor, for example 10.0 or even larger? In your constraint file you might need to add the constraint specifier “SCALARWEIGHTEDFUNC”. For example,
AtomPair OG 624 NE2 144 SCALARWEIGHTEDFUNC 10.0 BOUNDED 2.9 3.5 1.0 X
Also make sure that the residue numbering is based on the fasta file and not the PDB_id.
Hope this helps.
March 28, 2016 at 8:08 am #11492Anonymous
Sorry that I did not respond. Unfortunately I was not able to find out whether the constraints changed something, but thank you for your advice anyway
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