From 72c1030d6c7ae08de8a338533bb940a02a135dec Mon Sep 17 00:00:00 2001 From: Shruthi Viswanath Date: Wed, 5 Jun 2024 14:01:03 +0530 Subject: [PATCH] Update README.md --- examples/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/README.md b/examples/README.md index 667ff0a..3b4576f 100755 --- a/examples/README.md +++ b/examples/README.md @@ -7,7 +7,7 @@ The `examples/input` comprises of the fasta sequences (`examples/input/fasta`), In addition it also comprises the `topology{x}.txt` files that define the representation to be used for running the `nude_modeling.py` modeling script. The `{x}` in the topology file's name corresponds to the number of amino acid residues to be coarse-grained to a single flexible bead for regions that lack a previously characterized structure. In this example, we are comparing the 1, 5, 10, 20, 30 and 50 residues per bead coarse-grained representations of the regions with unknown structure of NuDe sub-complex. It is to be noted that the regions with known structure will be modeled as 1 and 10 residues per bead representation. Importantly, note that *any* representation can be compared as long there is a valid modeling file associated with it (representation can be mentioned via a topology file or manually). -It also contains the `examples/input/nestor_params_optrep.yaml` file which defines the NestOR parameters. Each parameter is described in the file itself. +It also contains the `examples/input/nestor_params_optrep.yaml` NestOR parameter file which defines the NestOR parameters. Each parameter is described in the file itself. The `nude_modeling.py` script is also adapted from the [Integrative model of the NuRD subcomplexes](https://github.com/isblab/nurd) repository for use with NestOR. @@ -16,5 +16,5 @@ The `nestor_output.yaml` contains an example output for the given setup. In addi ## Running nested sampling on this example For this example, the user may run NestOR as follows: ``` -python -m "IMP.wrapper_v{x} -p {path_to_param_file} +python -m "IMP.wrapper_v{x} -p {path_to_NestOR_param_file} ```