A question about Multiple constraints

[Anonymous]

Hi, all.
I’ve got a question about the Multiple Constraints, is there any differences between multiple-line constraints inside and outside a MultiConstraint block?
For example, if I want to apply two constraints, CST1 and CST2, what is the difference between the following two constraint files?

file1:
MultiConstraint
CST1
CST2
END

file2: (with out MultiConstraint block)
CST1
CST2

I am not sure if they are the same.

Anyone can help me? Thanks a lot in advance.

[Anonymous]

Nope, there isn’t any difference between those two options – at least within the top level of a constraint file.

The purpose of a MultiConstraint is to allow you to combine constraints in other locations, where a single constraint is expected. For example, if you wanted to have a MultiConstraint inside an Ambiguous constraint. For example

AmbiguousConstraint
MultiConstraint
CST1a
CST1b
END
CST2
END

and

AmbiguousConstraint
CST1a
CST1b
CST2
END

have very different behaviors. In the first, either (1a+1b) or 2 will be evaluated, but in the latter it’s just a single constraint from 1a or 1b or 2 which will be evaluated.

[Anonymous]

Hello,
I want to put some cs (.tab-format) and noe-contraints (upl-format form cyana) in the protocol. Which command should I use, when I put the constraints separably and both in the same protocol? For the first case the following commands doesn`t work:
-in:file:talos_cs .input/pax_talos_789456.tab
-constraints:cst_fa_file ./input/manualNOE.upl

[Anonymous]

Thanks a lot.

[Anonymous]

Hello again,

now I have problems with the module in Rosetta. The upl2rosetta can`t find “from basic.options import ExampleArgumentParser”, “import traceback, sys”, “import library”, “import fasta”. It feels like it must be a simple problem, but i don`t now how can I solve it. What can I do concretely to solve this problem?!

Where can I find, how the atoms for the noe-file must be numbered in the rosetta format?! I think its different to the cyana-file.

many regards

[Anonymous]

and is it possible to convert a Cyana-structure in a Rosetta structure ?! I want to use the cyana-structure as the native structure

[Anonymous]

Thanks a lot, rmoretti!

[Anonymous]

To my knowledge, Rosetta doesn’t understand upl-formatted NOE constraints. Instead, the file passed to -cst_fa_file is in it’s own file format. (See https://www.rosettacommons.org/docs/latest/constraint-file.html ) Usually AtomPair constraints with the BOUNDED functional form are used to specify that an NOE distance should fall somewhere between two specified values. As I understand it, CSRosetta has a upl2rosetta script which can help automate the conversion.

It looks like -in:file:talos_cs only is functional for the fragment picker. If you want to use chemical shifts during other protocols, you need to convert them. Again, CSRosetta should have scripts which will facilitate things.

[Author]

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