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about deNovoProteinMimeticsGen2
#1

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!

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Mon, 2019-01-14 17:09
zhangying1990

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

Mon, 2019-01-14 22:21
dsilva

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

 

Tue, 2019-01-15 00:25
zhangying1990

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

Tue, 2019-06-11 17:14
LH

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

Thu, 2019-02-21 07:40
tarsis

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.)

Thu, 2019-05-09 14:08
rmoretti

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

Wed, 2019-06-12 19:02
LH

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

Mon, 2019-06-24 12:37
rmoretti

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)

 

Tue, 2021-10-26 07:52
Maamoon Saleh