Symmetric design with PyRosetta

This topic has 27 replies, 3 voices, and was last updated 8 years, 1 month ago by Anonymous.

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- November 17, 2016 at 3:50 pm #2536
  Anonymous
  Hello,
  
  Is it possible to do symmetric design with PyRosetta4 ?
  
  I try to pass a symmetry flag to the command line and run pack_rotamers but I get a warning saying that I try to
  
  use a symmetric score function on a non symmetric protocol or something like that.
  
  In previous Rosetta versions, there was a symmetric_pack_rotamers, but this method disappeared and there is some symmetry code in
  
  the pack_rotamer method. Still, it doesn’t work. It works if I run fixxbb protocol though.
  
  I tried also this:
```
score_fxn = create_score_function(scorefunc)

mytask = TaskFactory.create_packer_task(pose)

mytask.initialize_from_command_line()

parse_resfile(pose, mytask, resfile)

pose.update_residue_neighbors()

png = create_packer_graph(pose, score_fxn, mytask)

mysymtask = make_new_symmetric_PackerTask_by_requested_method(pose,mytask)

rotsets = SymmetricRotamerSets()

pack_scorefxn_pose_handshake( pose, score_fxn);

rotsets.set_task( mysymtask )

rotsets.initialize_pose_for_rotsets_creation(pose)

rotsets.build_rotamers( pose, score_fxn, png )

rotsets.prepare_sets_for_packing( pose, score_fxn )
```
  But I get a segmentation fault in initialize_pose_for_rotsets_creation. Would anyone know why ?
  
  This piece of code is extracted from a script that works perfectly fine in non-symmetric mode.
- November 17, 2016 at 7:28 pm #11972
  Anonymous
  The reason for absense of symmetric_pack_rotamers is that it is no longer present in Rosetta C++ code. This is because regular pack_rotamers should be able now to handle symetric poses. Have you tried using it instead?
- November 17, 2016 at 7:28 pm #12493
  Anonymous
  The reason for absense of symmetric_pack_rotamers is that it is no longer present in Rosetta C++ code. This is because regular pack_rotamers should be able now to handle symetric poses. Have you tried using it instead?
- November 17, 2016 at 7:28 pm #13014
  Anonymous
  The reason for absense of symmetric_pack_rotamers is that it is no longer present in Rosetta C++ code. This is because regular pack_rotamers should be able now to handle symetric poses. Have you tried using it instead?
- November 17, 2016 at 8:50 pm #11975
  Anonymous
  If you have C++ code working – then it should definetely works in PyRosetta. Unless of course the C++ code is for different verion of Rosetta (for example if it have symmetric_pack_rotamers not yet removed). Could you please double check that your Rosetta C++ code version match/close to PyRosetta build?
- November 17, 2016 at 8:50 pm #12496
  Anonymous
  If you have C++ code working – then it should definetely works in PyRosetta. Unless of course the C++ code is for different verion of Rosetta (for example if it have symmetric_pack_rotamers not yet removed). Could you please double check that your Rosetta C++ code version match/close to PyRosetta build?
- November 17, 2016 at 8:50 pm #13017
  Anonymous
  If you have C++ code working – then it should definetely works in PyRosetta. Unless of course the C++ code is for different verion of Rosetta (for example if it have symmetric_pack_rotamers not yet removed). Could you please double check that your Rosetta C++ code version match/close to PyRosetta build?
- November 21, 2016 at 8:24 am #11977
  Anonymous
  It works with rosetta-3.7 and doesn’t work with PyRosetta4 release 117.
  
  Here is exactly what I do:
  
  I have a symmetry definition file and an imput files that were both generated by the rosetta perl script.
  
  I give both files to rosetta-3.7 fixxbb and it works. I can see from the log that it reads the symmetry definition properly.
  
  With PyRosetta4:
  
  I give the symmetry flag to the init() method
  
  I load the pose and the score function. Then I do this:
```
mytask = TaskFactory.create_packer_task(pose)

mytask.initialize_from_command_line()

parse_resfile(pose, mytask, resfile)

pack_rotamers(pose, score_fxn, mytask)
```
  and it says:
  
  core.scoring.symmetry.SymmetricScoreFunction: Warning!!! Using a symmetric score function on a non-symmetric pose
- November 21, 2016 at 8:24 am #12498
  Anonymous
  It works with rosetta-3.7 and doesn’t work with PyRosetta4 release 117.
  
  Here is exactly what I do:
  
  I have a symmetry definition file and an imput files that were both generated by the rosetta perl script.
  
  I give both files to rosetta-3.7 fixxbb and it works. I can see from the log that it reads the symmetry definition properly.
  
  With PyRosetta4:
  
  I give the symmetry flag to the init() method
  
  I load the pose and the score function. Then I do this:
```
mytask = TaskFactory.create_packer_task(pose)

mytask.initialize_from_command_line()

parse_resfile(pose, mytask, resfile)

pack_rotamers(pose, score_fxn, mytask)
```
  and it says:
  
  core.scoring.symmetry.SymmetricScoreFunction: Warning!!! Using a symmetric score function on a non-symmetric pose
- November 21, 2016 at 8:24 am #13019
  Anonymous
  It works with rosetta-3.7 and doesn’t work with PyRosetta4 release 117.
  
  Here is exactly what I do:
  
  I have a symmetry definition file and an imput files that were both generated by the rosetta perl script.
  
  I give both files to rosetta-3.7 fixxbb and it works. I can see from the log that it reads the symmetry definition properly.
  
  With PyRosetta4:
  
  I give the symmetry flag to the init() method
  
  I load the pose and the score function. Then I do this:
```
mytask = TaskFactory.create_packer_task(pose)

mytask.initialize_from_command_line()

parse_resfile(pose, mytask, resfile)

pack_rotamers(pose, score_fxn, mytask)
```
  and it says:
  
  core.scoring.symmetry.SymmetricScoreFunction: Warning!!! Using a symmetric score function on a non-symmetric pose
- November 21, 2016 at 7:07 pm #11983
  Anonymous
  The PyRosetta 117 is significantly more recent then 3.7 release so code is changed since then. I will try to ask develepers who familiar with this part of the code if there is a way around this.
- November 21, 2016 at 7:07 pm #12504
  Anonymous
  The PyRosetta 117 is significantly more recent then 3.7 release so code is changed since then. I will try to ask develepers who familiar with this part of the code if there is a way around this.
- November 21, 2016 at 7:07 pm #13025
  Anonymous
  The PyRosetta 117 is significantly more recent then 3.7 release so code is changed since then. I will try to ask develepers who familiar with this part of the code if there is a way around this.
- November 21, 2016 at 8:04 pm #11985
  Anonymous
  Well, I guess you are right. I wasn’t aware of any method to establish the pose as symmetric.
  
  I figured all this would be “automatic” since I specified some symmetry flag to the command line…
  
  I’ll give it a try and let you know. This may close the topic, thanks for your answers.
- November 21, 2016 at 8:04 pm #12506
  Anonymous
  Well, I guess you are right. I wasn’t aware of any method to establish the pose as symmetric.
  
  I figured all this would be “automatic” since I specified some symmetry flag to the command line…
  
  I’ll give it a try and let you know. This may close the topic, thanks for your answers.
- November 21, 2016 at 8:04 pm #13027
  Anonymous
  Well, I guess you are right. I wasn’t aware of any method to establish the pose as symmetric.
  
  I figured all this would be “automatic” since I specified some symmetry flag to the command line…
  
  I’ll give it a try and let you know. This may close the topic, thanks for your answers.
- November 22, 2016 at 4:10 pm #11986
  Anonymous
  It works, thank you guys.
  
  Actually the SymPackRotamersMover does everything I want.
- November 22, 2016 at 4:10 pm #12507
  Anonymous
  It works, thank you guys.
  
  Actually the SymPackRotamersMover does everything I want.
- November 22, 2016 at 4:10 pm #13028
  Anonymous
  It works, thank you guys.
  
  Actually the SymPackRotamersMover does everything I want.
- November 17, 2016 at 8:05 pm #11973
  Anonymous
  Yes I tried, sorry if my message wasn’t clear.
  
  I tried, and I got a warning which said that I was using a symmetric score function with a non symmetric protocol.
  
  I’ll post some more code about what I tried when I’m back in the lab tomorrow.
  
  It works fine with the c++ code, but I can’t make it work with pack_rotamer in the python version.
  
  I give the same symmetry options as when I run fixbb with the c++ version.
- November 17, 2016 at 8:05 pm #12494
  Anonymous
  Yes I tried, sorry if my message wasn’t clear.
  
  I tried, and I got a warning which said that I was using a symmetric score function with a non symmetric protocol.
  
  I’ll post some more code about what I tried when I’m back in the lab tomorrow.
  
  It works fine with the c++ code, but I can’t make it work with pack_rotamer in the python version.
  
  I give the same symmetry options as when I run fixbb with the c++ version.
- November 17, 2016 at 8:05 pm #13015
  Anonymous
  Yes I tried, sorry if my message wasn’t clear.
  
  I tried, and I got a warning which said that I was using a symmetric score function with a non symmetric protocol.
  
  I’ll post some more code about what I tried when I’m back in the lab tomorrow.
  
  It works fine with the c++ code, but I can’t make it work with pack_rotamer in the python version.
  
  I give the same symmetry options as when I run fixbb with the c++ version.
- November 17, 2016 at 8:06 pm #11974
  Anonymous
  .
- November 17, 2016 at 8:06 pm #12495
  Anonymous
  .
- November 17, 2016 at 8:06 pm #13016
  Anonymous
  .
- November 21, 2016 at 7:17 pm #11984
  Anonymous
  Possibly silly question, but have you properly initialized symmetry in your PyRosetta pose? That is, does core.pose.symmetry.is_symmetric( pose ) return True?
  
  If not, what have you done in your PyRosetta protocol to setup the pose for symmetry? Have you used core.pose.symmetry.make_symmetric_pose()? (http://graylab.jhu.edu/pyrosetta/downloads/documentation/PyRosetta_Tutorial_2012.pdf)
  
  Or did you use some other method to establish the pose as symmetric? For example, the fixbb application calls the protocols.simple_moves.symmetry.SetupForSymmetryMover on the pose prior to running the packer.
- November 21, 2016 at 7:17 pm #12505
  Anonymous
  Possibly silly question, but have you properly initialized symmetry in your PyRosetta pose? That is, does core.pose.symmetry.is_symmetric( pose ) return True?
  
  If not, what have you done in your PyRosetta protocol to setup the pose for symmetry? Have you used core.pose.symmetry.make_symmetric_pose()? (http://graylab.jhu.edu/pyrosetta/downloads/documentation/PyRosetta_Tutorial_2012.pdf)
  
  Or did you use some other method to establish the pose as symmetric? For example, the fixbb application calls the protocols.simple_moves.symmetry.SetupForSymmetryMover on the pose prior to running the packer.
- November 21, 2016 at 7:17 pm #13026
  Anonymous
  Possibly silly question, but have you properly initialized symmetry in your PyRosetta pose? That is, does core.pose.symmetry.is_symmetric( pose ) return True?
  
  If not, what have you done in your PyRosetta protocol to setup the pose for symmetry? Have you used core.pose.symmetry.make_symmetric_pose()? (http://graylab.jhu.edu/pyrosetta/downloads/documentation/PyRosetta_Tutorial_2012.pdf)
  
  Or did you use some other method to establish the pose as symmetric? For example, the fixbb application calls the protocols.simple_moves.symmetry.SetupForSymmetryMover on the pose prior to running the packer.
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