RosettaCommons - PyRosetta - Scripts

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Solved

%time results = list(xml_obj(pose_obj)) error

TENY BAEK — Thu, 03 Nov 2022 06:31:45 +0000

08.02-Ligand-Docking-pyrosetta.distributed.ipynb

When I ran the following syntax in this file, an error came out and it did not proceed.

if not os.getenv("DEBUG"):

%time results = list(xml_obj(pose_obj))

I also set up Conda on Google Collabor
There is an error, do you know how to solve it?

The results of the implementation were as follows

core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 50 EXCEEDED, BUT FUNC NOT CONVERGED!
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 50 EXCEEDED, BUT FUNC NOT CONVERGED!
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 50 EXCEEDED, BUT FUNC NOT CONVERGED!

---------------------------------------------------------------------------

NotImplementedError                       Traceback (most recent call last)

<timed exec> in <module>

/usr/local/lib/python3.7/dist-packages/pyrosetta/distributed/packed_pose/core.py in <genexpr>(.0)
    160         @generic_func.register(collections.abc.Generator)
    161         def generator_traversal(generator):
--> 162             return (generic_func(v) for v in generator)
    163 
    164     return generic_func

5 frames

/usr/local/lib/python3.7/dist-packages/pyrosetta/distributed/utility/pickle.py in __cereal_getstate__(self)
     35     if not cereal:
     36         raise NotImplementedError(
---> 37             "__cereal_getstate__ requires pyrosetta '--serialization' build.")
     38 
     39     oss = rosetta.std.ostringstream()

NotImplementedError: __cereal_getstate__ requires pyrosetta '--serialization' build.

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CONECT information for PDB files by raw sequence

Fata — Wed, 22 Jun 2022 08:47:25 +0000

Hello,

I create a pose from sequence and dump it as PDB:

pep_pose = pyrosetta.pose_from_sequence(sequence, res_type='fa_standard', auto_termini=True)
# pep_pose = pyrosetta.Pose()
# pyrosetta.rosetta.core.pose.make_pose_from_sequence(pep_pose, sequence, 'fa_standard', auto_termini=True)
pep_pose.dump_pdb(pdb_file_path)

As I understood, 'pose_from_sequence' creates a peptide structure by sequence, but what I found was that the PDB file misses the whole CONECT information.

How can I add the CONECTs to the output PDB file? I am still unsure, if the "bound" information is never created or simply not written during the pdb-dump.

Thanks,

Fabian

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Post Situation:

Solved

PackRotamersMover in another way

hlinn — Mon, 07 Feb 2022 15:10:48 +0000

I want to design peptides, allowing redesign and side-chain packing, but no backbone changes. So far I'm using PackRotamersMover, but I would like to write my packer with fixbb instead to have more control.

My question basically is: why do the two following snippets of code not do the same? And what have I missed about PackRotamersMover in my version?

code 1:

tf = TaskFactory()
tf.push_back(operation.InitializeFromCommandline())
packer = pack_min.PackRotamersMover(scorefxn)
packer.task_factory(tf)
packer.apply(pose)

code 2:

tf = TaskFactory()
tf.push_back(operation.InitializeFromCommandline())
mm = MoveMap()
mm.set_bb(False)
mm.set_chi(True)
fixbb = pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign()
fixbb.set_task_factory(tf)
fixbb.set_movemap(mm)
fixbb.set_scorefxn(scorefxn)

Category:

Design

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Post Situation:

Scripts accompanying Hossenzadeh et al, 2001

Ken — Wed, 19 Jan 2022 15:38:16 +0000

Hi all,

I recently came across the paper titled "Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites" and wanted to try it out for myself. I downloaded the supplemental materials and tried to follow along the READMEs to test out Methods 1-4. But I am not able to actually get any of them to work even with the provided pdbs. Is anybody else having the same problem?

Here is what I have tried...

For Method 1, I set up a conda environment for python2.7 and ran python ../main.py -f target.pdb --targetresidues "ALA 3" -q 8mer_ALA.pdb --queryresidues "ALA 370" which generated the realign8mer_ALA.pdb. So far so good.

I then edited the merge_8.xml script to use realign8mer_ALA.pdb and tried to run it and It gave me the first error in crash log.

I also tried adding the flag -input_empty_pose true as a flag and tit gave me the second error in the crash log.

I am attaching the xml file (as a txt) in case it was something silly and obvious.

Has anyone been able to get this to run?

Best,

Ken

Attachment	Size
crash log	3.96 KB
xml	1 KB

Category:

Design

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setup_foldtree not maintaining partners

alkaline_lemon — Fri, 30 Jul 2021 16:17:11 +0000

Hello all - brand new to using pyrosetta so apologies if I'm missing something obvious.

I'm currently in the process of trying to translate the code from the point mutation scan tutorial to my system (https://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb)

The system I'm working with has a total of five chains, with the first group being chains ABC and the second group being chains DE. For some reason, during the unbinding process these groups aren't being maintained. The code at current is formatted as:

def unbind(pose, partners):
STEP_SIZE = 100
JUMP = 2
setup_foldtree(pose,partners,Vector1([1]))
trans_mover = rigid.RigidBodyTransMover(pose,JUMP)
trans_mover.step_size(STEP_SIZE)
trans_mover.apply(pose)
unbind(relaxPose, "ABC_DE")

Depending on how I order the groups, either only chain D will translate from the complex (leaving a 100 angstrom disulfide to chain E..) or AB and DE will translate, leaving chain C hanging out in space. I've also tried running the script after editing the pdb to have chains D and E be one single chain, and I'm still running into the same issue. I've also tinkered around with Vector1 and had the same result as well. I've noticed that setup_foldtree adds a jumping edge between chains B and E, so I'm assuming during the jump it treats ABDE as a singular group. Has anyone run into a similar issue, or have any suggestions on how to fix this particular one?

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Post Situation:

How to make .frags files

krosika1 — Fri, 09 Jul 2021 01:16:59 +0000

Hello!

I am working through the online pyrosetta tutorial in jupyter notebooks, and they request you use files that are ".frags" files for ab initio structure prediction. Unfurtunately, all of the google drive files that come with the tutorial are no longer accessible (the link goes to a 404 error).

How do you create these .frags files for your POI? I tried using old robetta, but none of the "fragment" files produced have the .frags extension, nor can any of them be downloaded off of the internet. I would appreciate any help/advice!

Category:

Design

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Post Situation:

Error running D100_Docking.py

Rodriguez — Fri, 25 Jun 2021 18:32:35 +0000

Hello,

So I am trying to run the D100_Docking.py on PyRosetta4 that I have installed on Windows 10 Bash shell. I am just trying to use the script as is before attempting my own PDB files. Below is what I did, along with the errors:

Any help is greatly appreciated!

(base) jrodriguez@DESKTOP:/mnt/c/Windows/system32$ cd /mnt/c/Users/jrodriguez/Documents/PyRosetta4

(base) jrodriguez@DESKTOP:/mnt/c/Users/jrodriguez/Documents/PyRosetta4$ ls -la
total 796
drwxrwxrwx 1 jrodriguez jrodriguez 512 Jun 25 11:37 .
drwxrwxrwx 1 jrodriguez jrodriguez 512 Jun 23 09:18 ..
drwxrwxrwx 1 jrodriguez jrodriguez 512 Jun 25 11:36 .ipynb_checkpoints
drwxrwxrwx 1 jrodriguez jrodriguez 512 Jun 2 11:36 .test.output
-rwxrwxrwx 1 jrodriguez jrodriguez 158112 Jun 25 10:31 3RT3.clean.pdb
-rwxrwxrwx 1 jrodriguez jrodriguez 357939 Jun 25 10:18 3RT3.pdb
-rwxrwxrwx 1 jrodriguez jrodriguez 3303 Jun 25 10:33 Clean_Pose.ipynb
-rwxrwxrwx 1 jrodriguez jrodriguez 27412 Jun 25 11:36 Docking.ipynb
-rwxrwxrwx 1 jrodriguez jrodriguez 22463 Jun 25 11:36 Docking.py
-rwxrwxrwx 1 jrodriguez jrodriguez 49331 May 18 23:52 PyMOL-Rosetta-relay-client.python2.py
-rwxrwxrwx 1 jrodriguez jrodriguez 48465 May 18 23:52 PyMOL-Rosetta-relay-client.python3.py
-rwxrwxrwx 1 jrodriguez jrodriguez 44567 May 18 23:52 PyMOL-RosettaServer.py
-rwxrwxrwx 1 jrodriguez jrodriguez 44651 May 18 23:52 PyMOL-RosettaServer.python3.py
drwxrwxrwx 1 jrodriguez jrodriguez 512 May 18 23:52 apps
drwxrwxrwx 1 jrodriguez jrodriguez 512 Jun 20 08:03 demo
drwxrwxrwx 1 jrodriguez jrodriguez 512 Jun 25 10:45 inputs
-rwxrwxrwx 1 jrodriguez jrodriguez 18013 Jun 25 11:30 protein_docking.ipynb
-rwxrwxrwx 1 jrodriguez jrodriguez 9173 Jun 25 10:20 protein_docking.py
lrwxrwxrwx 1 jrodriguez jrodriguez 17 May 18 23:54 pyrosetta -> ./setup/pyrosetta
-rwxrwxrwx 1 jrodriguez jrodriguez 0 Jun 25 10:32 python
lrwxrwxrwx 1 jrodriguez jrodriguez 15 May 18 23:54 rosetta -> ./setup/rosetta
-rwxrwxrwx 1 jrodriguez jrodriguez 7272 May 18 23:52 self-test.py
drwxrwxrwx 1 jrodriguez jrodriguez 512 Jun 2 11:16 setup
drwxrwxrwx 1 jrodriguez jrodriguez 512 May 18 23:52 test
-rwxrwxrwx 1 jrodriguez jrodriguez 844 May 18 23:54 version.json

(base) jrodriguez@DESKTOP:/mnt/c/Users/jrodriguez/Documents/PyRosetta4$ python3 ./Docking.py --pdb_filename /mnt/c/Users/jrodriguez/Documents/PyRosetta4/3RT3.clean.pdb --partners B_C --jobs=1000 --job_output 3RT3_docking_output
./Docking.py:96: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.
from rosetta import *
PyRosetta-4 2021 [Rosetta PyRosetta4.Release.python38.linux 2021.20+release.47c4f8c41a32caced161a9246b20be0a5c576b75 2021-05-18T09:24:24] retrieved from: http://www.pyrosetta.org
(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: PyRosetta4.Release.python38.linux r283 2021.20+release.47c4f8c 47c4f8c41a32caced161a9246b20be0a5c576b75 http://www.pyrosetta.org 2021-05-18T09:24:24
core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /mnt/c/Users/jrodriguez/Documents/PyRosetta4/pyrosetta/database
basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 984 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 1.48438 seconds.
core.import_pose.import_pose: File '/mnt/c/Users/jrodriguez/Documents/PyRosetta4/3RT3.clean.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 153
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue PRO:CtermProteinFull 247
Traceback (most recent call last):
File "./Docking.py", line 366, in <module>
sample_docking(pdb_filename, partners, translation, rotation,
File "./Docking.py", line 152, in sample_docking
protocols.docking.setup_foldtree(pose, partners, Vector1([dock_jump]))
AttributeError: module 'pyrosetta.protocols' has no attribute 'docking'

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Docking

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Post Situation:

Argument Error while running Ligand_interface.py

Karthik — Sun, 14 Mar 2021 05:54:47 +0000

Hello,

I am facing trouble running the script ligand interface.py. I have prepared the pdb file and params file as instructed. I have also added the params file to the default directory and updated residue_types.txt file. The following error gets invoked. Please do help rectify the error.

Traceback (most recent call last):
File "LigandInterface.py", line 139, in <module>
sample_ligand_interface(pdb_filename, partners, ligand_params, jobs, job_output)
File "LigandInterface.py", line 30, in sample_ligand_interface
new_res_set = generate_nonstandard_residue_set(ligand_params)
File "LigandInterface.py", line 102, in generate_nonstandard_residue_set
res_set.read_files( params_list , atoms , mm_atoms , orbitals )
AttributeError: 'ResidueTypeSet' object has no attribute 'read_files'

I have attached the script below.

Attachment	Size
Ligand_Interface_script.txt	4.57 KB

Category:

Docking

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Is there a side-program enabling us to see the clashes and interactions between ligand and protein?

egecav — Fri, 05 Feb 2021 12:42:54 +0000

I'm currently working on a program where i may need to see clashes and interactions between ligand and the protein after PyRosetta-lead conformation. Is there such program?

Thanks!

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