RosettaCommons - Symmetry

Minimizing a Symmetric Structure

ammar.x.gilani — Wed, 02 Aug 2023 18:10:50 +0000

Hi, I have a structure with two chains (1 and 2 ) which are identical. My goal is to minimize its structure using FastRelax with a symmetry constraint.

Creating symmetry file:

make_symmdef_file.pl -p Data/2mcg.pdb -a 1 -i 2 > Data/2mcg.symm

Structure minimization:

import pyrosetta
from pyrosetta import rosetta

id = '2mcg'

pose = pyrosetta.pose_from_pdb(f'Data/{id}_symm.pdb')
symm_data = pyrosetta.rosetta.core.conformation.symmetry.SymmData()
symm_data.read_symmetry_data_from_file(f'Data/{id}.symm')
pyrosetta.rosetta.core.pose.symmetry.make_symmetric_pose(pose, symm_data)

rel = rosetta.protocols.relax.FastRelax()
rel.apply(pose)  # Segmentation Fault

But I get segmentation fault at the line specified above.

Moreover, I get the following error when I score the symmetric pose:

import pyrosetta
from pyrosetta import rosetta

id = '2mcg'

pose = pyrosetta.pose_from_pdb(f'Data/{id}_symm.pdb')
symm_data = pyrosetta.rosetta.core.conformation.symmetry.SymmData()
symm_data.read_symmetry_data_from_file(f'Data/{id}.symm')
pyrosetta.rosetta.core.pose.symmetry.make_symmetric_pose(pose, symm_data)

scorefxn = pyrosetta.get_fa_scorefxn()
scorefxn(pose)  # Error Line

RuntimeError: 

File: CountPairFactory.cc:220
[ ERROR ] UtilityExitException
ERROR: Assertion `res2.is_bonded(res1)` failed.

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Symmetry definition question

mrconde96 — Sun, 02 Oct 2022 12:34:40 +0000

Hello!

I'm relatively new to Rosetta and I'm trying to apply symmetry in the BlueprintBDR. As I only know that I want C3 symmetry I used the general symmdef file for this symmetry. Still, I noticed that it just rotates the subunits with no translation from the COM of the arrangement, which leads to an overlap in residue coordinates, which in turn leads to problems in the minimization protocol. I have attached a picture of an example of what I got and the symmdef file used to obtain it.

Any help is greatly appreciated!

Attachment	Size
image.png	114.99 KB
c3.symm_.txt	349 bytes

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Rosetta 3 - Applications

Weekly releases for commercial users?

rjacak — Tue, 22 Mar 2022 14:48:27 +0000

Hi Steven, Rocco, et al.,

Would it be possible to have the weekly releases for commercial users restarted? The last weekly release available (for commercial users, maybe commercial and academic users?) is Rosetta 2021.16, with a release date of Friday, April 23, 2021. I know there have been bug fixes and other minor improvements made to apps that I am using and it would be great to have access to those. If weekly releases are unlikely to restart anytime soon, would it be possible to have the source code changes of bug fixes merged into main (master) posted somewhere so that licensees can patch the source themselves?

Thanks,
-Ron

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Chemically Modified Residues

Fragment Generation

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Symmetry definition file versions

Jeff Qu — Tue, 28 Sep 2021 16:53:36 +0000

When I tried to generate the symmetry definition file of 6ufr, which is helical symmetry (I used the parameter -m HELIX -a A -b D -i B -t 2 -r 20). And I found out that the Perl script on our school's computing clusters and mine are different(one produce @fakePDBlines and the virtual residues are different). So I am wondering about which one is the newest version since they produce different jumps and different virtual residues. Besides, I am also wondering whether the 2 output structures and the jumps are the same energy. So did anyone have the same issue or recognize that? I cannot see an update log about the change.

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Symmetry breaks due to small structure gaps

dbiedermann — Tue, 21 Sep 2021 00:39:45 +0000

Hi everyone,

I'm having trouble re-designing a 2-component symmetric nanoparticle with small gaps along lines that connect symmetry axes. The starting pdb looked good, so I selected 2 chains that define the unit cell and apply a symmetry file to enable the computational savings associated with symmetry. However, the symmetric docking step that's triggered by the rosetta.protocols.symmetry.SetupForSymmetryMover method seems to smush the chains together, resulting in a smaller radius nanoparticle with VdW clashes.

I've tried a few things but nothing's worked so far. I tried to start from the assembled structure and supply the symmetry info directly using:

sd = pyrosetta.rosetta.core.conformation.symmetry.SymmData()
rosetta.core.conformation.symmetry.SymmData.read_symmetry_data_from_file(sd,"my_simfile.sym")

pyrosetta.rosetta.core.pose.symmetry.make_symmetric_pose(big_pose,sd)

I also tried to figure out how to replace the atom tree of the symmetric pose with the positions from the original pose, but couldn't figure out how to do this from the documentation. Does anyone know of a workaround that I could use for this issue?

Thanks, any help would be greatly appreciated!

Drew

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Symmetry

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PyRosetta - General

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calcium metal nomenclature: Rosetta_cm confusing HETATM CA (calcium) with ATOM CA (alpha-carbon)

rlwoltz — Wed, 04 Aug 2021 06:26:29 +0000

Dear community,

I had this posted under a different sub-forum but I realized it didn't fit that forum so deleted it and reposting here.

Hopefully this is a simple answer but I couldn't find any answer and I don't remember this happening on a previous rosetta version, just updated from 2019 to 2021.16.61629_bundle. The goal is to add constraints to the amino acids that bind calcium in a homology model since they are in a small loop and can reorient without calcium present. I'm using the metal_setup mover to apply constraints but I'm open to other suggestions.

I'm doing a homology model of a 4-unit symmetrical membrane channel coupled with Calmodulin. The channel and Calmodulin are seperate chains which is denoted in the fasta with a "/" in the sequence to show the split. All this works fine for un-calcified calmodulin. However, now I'm making a calcified calmodulin structure and I have calcium ions in the single unit INPUT.pdb (output of make_symm.sh file. The thread is made with no issue. The problem is the next step of using rosetta_CM and the xml. I'm using the metals setup mover line (1) to denote the amino acids and residues. However, the calcium ions are being confused by roestta for Alpha-Carbons. I have three Calciums per subunit and they are all being overlayed onto the last alpha carbon in the protein sequence for each single unit (2).

Is there a special residue or atom name the rosetta is expecting for Calciums? currently the only naming scheme that works is "CA". (3)

Thanks for any help and let me know if you need any more information,

Ryan

1. calcium is residues 526-528. interacting residues is 397-408 --> 526, 433-433 --> 527, 470-480 --> 528

2. notice that the Calciums have the same coordinates as the first alpha-carbon of chain B the start of calmodulin. this is true for all 4 symmetrical units

ATOM 6185 OD1 ASN A 379 -2.989 8.407 56.731 1.00 0.00 O
ATOM 6186 ND2 ASN A 379 -3.678 8.654 54.615 1.00 0.00 N
ATOM 6187 H ASN A 379 -5.605 5.733 55.922 1.00 0.00 H
ATOM 6188 HA ASN A 379 -4.757 7.483 58.184 1.00 0.00 H
ATOM 6189 1HB ASN A 379 -5.936 8.097 55.462 1.00 0.00 H
ATOM 6190 2HB ASN A 379 -5.666 9.317 56.708 1.00 0.00 H
ATOM 6191 1HD2 ASN A 379 -2.719 8.727 54.264 1.00 0.00 H
ATOM 6192 2HD2 ASN A 379 -4.442 8.704 53.978 1.00 0.00 H
TER
ATOM 6194 N ASP B 380 -1.237 -47.247 33.849 1.00 0.00 N
ATOM 6195 CA ASP B 380 -2.006 -46.260 34.601 1.00 0.00 C
ATOM 6196 C ASP B 380 -2.779 -45.354 33.619 1.00 0.00 C
ATOM 6197 O ASP B 380 -3.335 -45.841 32.634 1.00 0.00 O
ATOM 6198 CB ASP B 380 -1.035 -45.467 35.514 1.00 0.00 C
ATOM 6199 CG ASP B 380 -1.668 -44.574 36.608 1.00 0.00 C
ATOM 6200 OD1 ASP B 380 -2.103 -44.975 37.659 1.00 0.00 O
...

HETATM 8425 CA CA C 526 -2.006 -46.260 34.601 1.00 0.00 CA
HETATM 8426 CA CA C 527 -2.006 -46.260 34.601 1.00 0.00 CA
HETATM 8427 CA CA C 528 -2.006 -46.260 34.601 1.00 0.00 CA

3. last few lines of input file. notice no TER line although I've tried it with. notice different XYZ coordinates for all atoms. I've also tried adjusting the spacing of the "CA" in the residue column. Calmodulin for the input as chain A but converted to chain B due to the fasta file input described above.

ATOM 5840 CA ASP A 380 -5.804 -51.544 37.679 1.00 0.00 C
...

ATOM 8068 3HB ALA A 525 -34.729 -39.328 36.187 1.00 0.00 H
HETATM 8069 CA CA A 526 2.182 -32.441 49.215 1.00239.49
HETATM 8070 CA CA A 527 -8.813 -37.633 50.564 1.00182.89
HETATM 8071 CA CA A 528 -33.639 -23.142 47.008 1.00223.54

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FastRelax Mover with symmetry, ligand and membrane

Michele.Bonus — Wed, 26 May 2021 11:43:44 +0000

Dear all,

I am currently trying to run the FastRelax Mover in RosettaScripts to relax a C4-symmetric protein with 4 ligands (1 per monomer). My input structure is a single protomer and a ligand (the pdb file unfortunately exceeds the maximum file size). My xml and option files look as follows. Note that I don't actually use the MembranePositionFromTopologyMover because it fills up 16 GB of memory pretty quickly. This leads to my first question. Can I just omit this mover if the protein is reasonably aligned and I specify a spanfile in the (Symmetric)AddMembraneMover?

XML File:

<ROSETTASCRIPTS>
    <TASKOPERATIONS>
        <RestrictToRepacking name="restrict"/>
        <IncludeCurrent name="keep_curr"/>
    </TASKOPERATIONS>
    <SCOREFXNS>
        <ScoreFunction name="memb_hires" weights="%%sfxn_weights%%"/>
    </SCOREFXNS>
    <FILTERS>
    </FILTERS>
    <MOVERS>
        <SetupForSymmetry name="setup_symm" definition="mHCN2_from_6UQG_07_S_0001.symm" set_global_symmetry_at_parsetime="0"/>
        <SymmetricAddMembraneMover name="add_memb" spanfile="mHCN2_from_6UQG_A.span"/>
        <MembranePositionFromTopologyMover name="init_pos"/>
        <FastRelax name="fast_relax" scorefxn="memb_hires" repeats="8"/>
    </MOVERS>
    <APPLY_TO_POSE>
    </APPLY_TO_POSE>
    <PROTOCOLS>
        <Add mover="setup_symm"/>
        <Add mover="add_memb"/>
        <!--Add mover="init_pos"/-->
        <Add mover="fast_relax"/>
    </PROTOCOLS>
    <OUTPUT scorefxn="memb_hires"/>
</ROSETTASCRIPTS>

Options file:

-in:file:s mHCN2_from_6UQG_07_S_0001_INPUT.pdb
-in:file:extra_res_fa ../04_Threading/04_Ligand_Parameters/CMP.fa.params
-parser:script_vars sfxn_weights=franklin2019
-mp:setup:spanfiles mHCN2_from_6UQG_A.span
-parser:protocol mHCN2_from_6UQG_relax.xml
-out:file:scorefile model_scores.sc
-mp:lipids:composition DLPC
-out:pdb
-relax:jump_move true
-relax:fast
-packing:pack_missing_sidechains false
-score:weights franklin2019

In any case, RosettaScript exits with a rather uninformative error unless I delete the ligand from the PDB file.

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.


terminate called after throwing an instance of 'std::out_of_range'
  what():  map::at
Got some signal... It is:6
Signal 6 (SIGABRT) means that the process was aborted.  This usually means an internal Rosetta error caused by (often) bad inputs, (sometimes) developer error, or (rarely) hardware problems.

Next, I figured, I should add the Ligand to the pose using the AddMPLigandMover, so I changed my XML file accordingly:

[...]
    <MOVERS>
        <SetupForSymmetry name="setup_symm" definition="mHCN2_from_6UQG_07_S_0001.symm"/>
        <SymmetricAddMembraneMover name="add_memb" spanfile="mHCN2_from_6UQG_A.span"/>
        <AddMPLigandMover name="add_lig" ligand_seqpos="1" closest_rsd="450"/>
        <MembranePositionFromTopologyMover name="init_pos"/>
        <FastRelax name="fast_relax" scorefxn="memb_hires" repeats="8"/>
    </MOVERS>
    <APPLY_TO_POSE>
    </APPLY_TO_POSE>
    <PROTOCOLS>
        <Add mover="setup_symm"/>
        <Add mover="add_memb"/>
        <Add mover="add_lig"/>
        <!--Add mover="init_pos"/-->
        <Add mover="fast_relax"/>
    </PROTOCOLS>
    <OUTPUT scorefxn="memb_hires"/>
</ROSETTASCRIPTS>

Unfortunately, RosettaScripts didn't like the idea of adding a ligand to an already symmetric membrane pose. It seems the AddMPLigandMover can only add ligands to non-symmetric membrane poses (I checked this on the monomer and it worked).

In thinking of a workaround, I decided to add a membrane to the monomer pose first, add the Ligand with the AddMPLigandMover, then SetupForSymmetry and then run FastRelax. This worked, the protein looks ok (despite a lot of "inaccurate G! step" warnings) and the ligand is there in all four protomers. Here is the final working XML file:

<ROSETTASCRIPTS>
    <TASKOPERATIONS>
        <RestrictToRepacking name="restrict"/>
        <IncludeCurrent name="keep_curr"/>
    </TASKOPERATIONS>
    <SCOREFXNS>
        <ScoreFunction name="memb_hires" weights="%%sfxn_weights%%"/>
    </SCOREFXNS>
    <FILTERS>
    </FILTERS>
    <MOVERS>
        <AddMembraneMover name="add_memb" spanfile="mHCN2_from_6UQG_A.span"/>
        <AddMPLigandMover name="add_lig" ligand_seqpos="580" closest_rsd="450"/>
        <SetupForSymmetry name="setup_symm" definition="mHCN2_from_6UQG_07_S_0001.symm"/>
        <FastRelax name="fast_relax" scorefxn="memb_hires" repeats="1"/>
    </MOVERS>
    <APPLY_TO_POSE>
    </APPLY_TO_POSE>
    <PROTOCOLS>
        <Add mover="add_memb"/>
        <Add mover="add_lig"/>
        <Add mover="setup_symm"/>
        <Add mover="fast_relax"/>
    </PROTOCOLS>
    <OUTPUT scorefxn="memb_hires"/>
</ROSETTASCRIPTS>

Since i symmetrize after adding the membrane, I now have 4 MEM residues that seem slightly different (see attachment). Although the protein looks OK, I have doubts about the results because of this. Is there any "non-workaround" solution that I should clearly be using here? I couldn't find any AddMPLigandMover equivalent that works on symmetric poses.

I would appreciate any help!

Best regards

Michele

Attachment	Size
1.jpg	315.34 KB
2.jpg	208.93 KB

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MPI optimization on TACC stampede2 HPC

rlwoltz — Wed, 17 Mar 2021 01:07:26 +0000

Dear community,

I am new to MPI so please correct any misuse of terms. My question is about optimizing for MPI on an HPC or a second (preferred) solution to my issue is to optimize my RAM usage so I don't have to run MPI, serial would actually improve overall models produced anyways.

First I have a very simple question, in the output of rosetta how do I know how many cores are being used in the MPI? I see (0), (1), and (2) at the beginning of each line so I'm assuming this mean 1 2 and 3 cores being used for that output line, is this correct? Basically if I'm using 2 cores with MPI in the output how do I know they actually got used?

I'm trying to optimize my rosetta MPI run on an HPC and my code currently is running 3X slower than expected and from reading documentation I think it just might be an option incompatibility so hoping someone with experience can advise. I have a lot of experience running with HPCs charging by the CPU but I'm using stampede2 which charges by the node so things get complicated here. Normally I'd prefer to run completely in serial but the maximum RAM the node has is 96GB and my system uses 3GB per run limiting me to about 35 runs per node (emperically tested this) but I have 68 available cores thus the want to include MPI to take advantage of the 36 idle cores (assuming I play it safe and only run 32 runs/node). Again with the HPC I'm using you can only request an entire node not individual CPUS.

So this is my plan of attack:

Request 1 node which has 96GB of RAM and 68 Xeon PHI CPUs. run 32 independent jobs to prevent exceeding RAM but each job will have 2 CPUs working in MPI.

programs I'm using to submit (screenshots attached):

I have 4 scripts that pass things along. First I have my sbatch submission script which uses the launcher module. The main objective in this is to request 32 tasks to be run at a time with 2 CPUs per task. Then I have a jobfile that essentially lists the total number of commands (tasks) I'd like to run, for example 320 tasks would run 10 rosetta runs on 32 (X 2 for MPI) CPUs in parallel and independently. This job file runs the rosetta command file which must use mpiexec (not mpirun) command explained below. Finally this also calls the rosetta.xml but this doesn't really play a role in the sbatch but it is there for completeness.

Double checking run:

When checking top on the node the job is submitted to 65 CPUs are in use (64 for rosetta jobs and 1 for node managment?). However, I do notice that there are 2474 total, 61 running and 2413 sleeping so not sure what this refers to maybe threads (NOTE: these numbers are for my latest 30 CPU test not 32 as I'm describing)? Unfortunately, top is the only montoring program (I use htop) so if there is a command that can be used to officially check the CPUs being used I'd appreciate it. also in the rosetta output it has a (0) and a (1) for each line. I'm assuming this refers to 1 or 2 cpus being used but please clarify if I'm wrong. When I tested with 4 CPUs the max number I saw was (2) so maybe a solution is to run 22 tasks and MPI CPU=3?

output files (don't think it is helpful for troubleshooting but might be helpful in advising where to ask me to start looking):

Jobfile also has the rosetta terminal output saved with a file embedded with a unique stampede2 job id, launcher job # (1-320), and a launcher task id which I believe is the CPU id number running the script. Each Rosetta output silent files also has these unique embedded codes and saves all silent files to unique results directory.

The problem:

So everything runs and I believe it is doing MPI in the way that I'd like it to but don't know how to check other than the (x) line mentioned above. But it is very ineffecient and takes about 13 hours versus 4-6 hours per model on my laptop. I'm doing a homology model with symmetry, membrane, and loops of a protein that is 2100 AA in total and I've spent a lot of time optimizing this part. My preference obviously is to run completely in serial but because of RAM limitations this isn't possible. I'd assume the MPI would be faster, not 3X slower, than serial so I'm just wondering if I can optimize the options here. I read this about "bind to none" option in openmpi but again I've never dealt with MPI and so the terminaology is difficult for me to understand. Again in the top there are a lot of sleeping tasks so this is why I think it could be optimized. I've attached screenshots of the slurm submission script, the jobfile script, and the mpiexec rosetta run script.

Possible solutions:

I've played around with options but because of the queue and the 13 hours to make a model it is taking days-weeks to get any meaningful results. I did test with a shorter 5 min run but it didn't scale. I'm continueing to try new things but thought I could save time by asking for advice. I have a feeling it has something to do with either the launcer slurm script or the way I'm calling for MPI. The launcher slurm script calls for -n = 32 # number of tasks ---cpus-per-task=2. In the rosetta MPI running file I have this line:

mpiexec.hydra -genv I_MPI_FALLBACK=1 -n 2 rosetta_scripts.cxx11mpi.linuxiccrelease \

-genv I_MPI_FALLBACK=1 #must be included otherwise the job fails. Something with Fabric and fallback disabled so don't understand this bit but included because it works.

-n 2 #number of cpus per task? but the document I read suggested this is how many time the command is run so I'm confused by this, maybe it should be 32?

There is also this passage:

Please note that mpirun automatically binds processes as of the start of the v1.8 series. Three binding patterns are used in the absence of any further directives:

Bind to core:: when the number of processes is <= 2
Bind to socket:: when the number of processes is > 2
Bind to none:: when oversubscribed; It sounds like I should bind to core since I'm running with 2 but really I'm running with 32X2 so should I bind to none?; MPIrun document:; https://www.open-mpi.org/doc/v3.0/man1/mpirun.1.php; Sorry if this isn't a problem so much as helping me improve my code and unfortunately no one in my network has experience running rosetta in MPI.

Thank you for your help and please let me know if more information or clarification is needed,

Ryan

Attachment	Size
launcher slurm	287.08 KB
jobfile launcher	491.5 KB
rosetta mpi script	310.21 KB

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Metal Ion in symmetric design

tschiex — Wed, 08 Jul 2020 12:28:24 +0000

I would like to run a design protocol on a protein that has, as its asymmetric unit, 2 proteins with an ion. I have done some purely AA-based symmetric design before with 2 chains controlled by separate virtual jumps and my own python-generated symdef file but I'd rather avoid doing that again :-)

My hope was that I could put (even if suboptimal) the 2 chains and the ion in a single chain and proceed as usual in symmetric design with one chain.

This works fine with the 2 proteins as a single chain but as soon as I include the metal ion in the chain, the generated symmetric structure is bad (and Vikram's metal flag doesn't help). Apparently, new jumps are created and this breaks everything.

To better understand this, would anybody have an example (pdb+symdef) of a simple symmetric structure with a metal ion at the interface of the ASU ? Or any advice otherwise.

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Structure refinement for helical assembles using Rosetta

xiaoyanzi — Thu, 18 Jun 2020 07:34:15 +0000

Hi all, I'm very new using Rosetta to make structure refinement. I'v read lots of related articles and also read the Tutorial: Rosetta tools for structure determination in cryoEM density. But I still not sure how to start my first Rosetta try. I have a helical map with about 3.9 angstrom resolution. The asymmetric unit for this helical structure is a tetramer. And the structure also has D5 symmetry except helical symmetry. I have generated the symmetry file using the tool "make_symmdef_file.pl". The rosetta script the .xml suffix was same as the one in the protocol. I have the following questions: 1. When I tried to run the refinement script, I can get just one refinement pdb file named "3tetramers_INPUT_symm_0001.pdb". I thought I need to get lots of pdb files like *_symm_????.pdb. Then I select the best one as my result. But now I only get one. I don't know where I'm wrong. How can I get lots of optimized pdb files with different scores? 2. I know there many score functions and mover in the xml script. How can I know which score function and which mover should I select to use? 3. On the other hand, I'm also not sure how shall I prepare the start pdb file? The asymmetric unit is tetramer with 4 chains, I renamed them uniformly as one chain. Is this ok? If not so, I found it is difficult for me to generate the symmetry files which is necessary for symmetry refinement. Sorry for so many naive question. Any suggestion or help are appreciated. Related file was attached. Thanks in advance. Regards, Yan

Attachment	Size
a.xml_.log	2.69 KB

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