Member Site › Forums › Rosetta 3 › Rosetta 3 – General › A question about Multiple constraints
- This topic has 7 replies, 3 voices, and was last updated 9 years, 8 months ago by
Anonymous.
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June 16, 2014 at 2:02 pm #1915
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
ENDfile2: (with out MultiConstraint block)
CST1
CST2I am not sure if they are the same.
Anyone can help me? Thanks a lot in advance.
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June 16, 2014 at 3:31 pm #10096
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
ENDand
AmbiguousConstraint
CST1a
CST1b
CST2
ENDhave 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.
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October 27, 2014 at 11:54 am #10487
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 -
November 19, 2014 at 8:49 am #10602
Anonymous
Thanks a lot.
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December 3, 2014 at 3:14 pm #10668
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
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December 19, 2014 at 4:30 pm #10717
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
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June 17, 2014 at 2:00 am #10097
Anonymous
Thanks a lot, rmoretti!
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November 4, 2014 at 12:17 am #10526
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.
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