about deNovoProteinMimeticsGen2

[Anonymous]

Good morning everyone~ 

Recently, I had read the paper entitled “De novo design of potent and selective mimics of IL-2 and IL-15”

And I am very interesting in it, and I want to learning how to performing it in using pyrosetta. 

However, in the Code availability section, I can not find any information about the submodule 

‘pyrosetta_scripts/apps/deNovoProteinDesign/deNovoProteinMimeticsGen2/’ . Even I download the newest weekly version(rosetta_src_2018.48.60516_bundle) and pyrosetta(PyRosetta4.Release.python27.mac.release-206).

Are there some one tell me how can i found these script?

Thank you!

[Anonymous]

Hi,

Sorry (for the delay), you are looking in the right place. Aka this:

pyrosetta_scripts/apps/deNovoProteinDesign/deNovoProteinMimeticsGen2

But, I forgot to push my commit to origin earlier, so it is now delayed.

It has been pushed now, it will def-come out with the next release. Sorry.

(BTW: It has a HOWTO that explains how to run a completely worked-out example)

Best,

Daniel

 

commit fd8934afab2797b48754dfb6df2eed537b5b9e92

Merge: b52f26b 24873cd

Author: dadriano <dadriano@mia.local>

Date:   Mon Jan 14 21:54:35 2019 -0800

    Merge remote-tracking branch ‘origin/master’ adds: deNovoProteinMimeticsGen2

    Added DeNovoProteinDesign deNovoProteinMimeticsGen2 algorithm

    Refers to Nature publication doi: 10.1038/s41586-018-0830-7

    De novo design of potent and selective mimics of IL-2 and IL-15

    D-A Silva, S Yu, U Y. Ulge, J B. Spangler, et.al., 01/10/2019, Nature

[Anonymous]

Thank you for your reply！ Looking forward to studying on it！！！

 

[Anonymous]

Hi, Daniel

I can not find the submodule ‘pyrosetta_scripts/apps/deNovoProteinDesign/deNovoProteinMimeticsGen2/’ in Pyrosetta4.release.python27.ubuntu.release-224. 

Can you tell me where I can find it? 

Thank you very much!

Best,

Hui

[Anonymous]

Hi,I’m getting the following error after removal of ” <CavityVolume name=”cav_vol_disabled” />” from deNovoPreprofiledMimeticsDesign_gen2.xml

###########

Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job ‘d9d67fad_2b5i_IL2only_renum_dlooperf_s00030015_c2b5i_rBGonly_renum_36187dfe_0001’

Error: [ ERROR ] 

File: src/protocols/filters/BasicFilters.cc:534

[ ERROR ] UtilityExitException

ERROR: Assertion `find_filter != filters.end()` failed.

############

As I do not have the cavity volume after checking this https://www.rosettacommons.org/node/10057 I would like to know if there’s a fix to this script.

Thanks,

Tarsis

[Anonymous]

If you remove the definition of the CavityVolume filter, you also have to remove any usage of it. (Look for lines which have “cav_vol_disabled” in them.)

[Anonymous]

Hello, 

I can not find the submodule ‘pyrosetta_scripts/apps/deNovoProteinDesign/deNovoProteinMimeticsGen2/’ in Pyrosetta4.release.python27.ubuntu.release-224. 

Who can tell me where I can find it? 

Thanks!

Best,

Hui

[Anonymous]

I’m not sure if the pyrosetta_scripts directory is distributed with the standard PyRosetta distribution. It can, though, be found with the recent released of command line Rosetta, which can be downloaded from https://www.rosettacommons.org/software/license-and-download

[Anonymous]

Howdy Everyone!

I hope all is well,  I’m a research intern at UNMC (University of Nebraska Medical Center), and after reading this article I was curious on running the algorithm myself. However, I ran into an error on line 632 of the, “protein_mimic_designer_r2_00b_libs.py”. 

The error reads:

ValueError: Invalid shape in the fixed-type tuple.

 

After looking around on stack overflow I wasn’t able to find anything that could fix the issue, I’m hoping someone can help me with what I’m missing

I’m using python3.7 to run the script— I converted both scripts from python 2 to 3 using the “2to3” package— and am running this on a MacBook 2017.  I will attach a photo below of the error and corresponding part of the pyrosetta script. 

Thank you so much for your time in advance, and I look forward to working with this algorithm some more 

 

The corresponding python script the error refers too:

        def get_fragment_entry_dtype(num_fragment_atoms):

                frag_size=num_fragment_atoms/len(atom_types_arr)

                return np.dtype([(“assignment”, np.int), 

                                        (“size”, np.int),

                                        (“avg_distance”, np.float), 

                                        (“threshold_distance”, np.float), 

                                        (“cordinates”, np.float, (num_fragment_atoms, 3)), 

                                        (“bb”, np.float, (frag_size, 3)), 

                                        (“ss”, np.float, (frag_size, 3)),

                                        (“aa”, np.float, (frag_size, 20)), 

                                        (“aa_w”, np.float, (frag_size, 20))])  (line 632)

 

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