RosettaCM Biological Assembly

[Anonymous]

Hi everyone,

Guys, I’m using rosettaCM, the problem is that I use a structure that is partially formed in the PDB (the rosettaCM queries the PDB to create the files) when it makes this query takes into account only part of the structure, does anyone know tell me what I change the setup_rosettaCM.py so that it takes into account the biology unit (Biological Assembly).

 

thaks

[Anonymous]

The setup_rosettaCM.py script allows for automatic setup of the RosettaCM protocol, but you can certainly put together the protocol manually, or adjust the automatically setup protocol for your particular case.

There’s a tutorial for manually putting together a RosettaCM protocol at http://meilerlab.org/index.php/jobs/resources under the Rosetta Tutorials tab and “New tutorials from December 2014” section. This is focused on membrane proteins (hence the need for manual setup), but the general process can be extended to soluble proteins.

Using the tutorial as a guideline on how a RosettaCM protocol is set up, you should be able to manually add your biological assembly to the templates which are used for your protocol.

[Anonymous]

Hi RMORETTI, thaks again.

I searched the entire file and protocol and have not found a way to solve my problem in any required form.

[Anonymous]

Okay. The automatically produced output files are a good starting point – I’d recommend adjusting them to get what you want.

As I understand your situation, you want to include an additional temlate in your run, or alter which templates you wish to use.

Take a look at the XML file that the script produces. In the Hybridize mover there should be multiple tags, one each for each template. Those are what specifies the templates you’re using during the actual run. What you need to do is change/add them to include your new templates.

The trick is that you can’t use a template PDB as-is; instead you need a pre-threaded version of your protein on the template. To do this, you should take your template structure and a Grishin-formatted alignment between your template and target, and pass them to the partial_thread application. (See the tutorial I mentioned for details on how to do this.) This will produce the requisite partially-threaded structure that can be used in the tag.

[Anonymous]

Hello RMORETTI.

Following the site (http://www.meilerlab.org/index.php/jobs/resources) of the tutorial’s instructions I had problems in two situations.

1) b. Thread target sequence over three individual template sequences.

Rosetta’s partial thread application will generate pdb’s for each alignment target-template by assigning coordinates

from the template PDB onto the aligned residues in the target sequence. This will be run once for each target-template

alignment and will result in three threaded .pdb files.

the files that should be generated in this step give error during the process with this msg

partial_thread:

partial_thread: id = 3vvt> 3vvt

partial_thread: Error: can not find pose (id = 3vvt)

2) I burlei that step and went to the next

Run RosettaCM hybridize

and I got this error msg

protocols.hybridization.HybridizeProtocol: Sequence mismatch between input and template fasta 3vvtCH1_on_3vvt.pdb at residue 1001

protocols.hybridization.HybridizeProtocol: Expected: L Saw: M

ERROR :: Exit from: src / protocols / hybridization / HybridizeProtocol.cc line: 773

Error: ERROR: Exception caught by JobDistributor while trying to get from job pose ‘S_0001’

Error:

[ERROR] EXCN_utility_exit Has Been thrown from: src / protocols / hybridization / HybridizeProtocol.cc line: 773

Error: failure Treating the bad input; canceling similar jobs

protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: S_0001

protocols.jd2.JobDistributor: no more batches to process …

protocols.jd2.JobDistributor: 3 Considered jobs, jobs first attempted in 23 seconds

Error: ERROR: Exception caught by rosetta_scripts application: 1 failed jobs; Check output for error messages

Error:

What do you think you can be?

[Anonymous]

On the second question, it looks like that’s a direct result of the failure of the first question. In order for the rosetta_scripts run to work correctly, it needs to have the threaded files – that is, the input PDBs for the templates need to have the desired sequence on them. If you don’t have that, then the program will choke due to the sequence mis-match.

On the first issue, the naming of the PDBs you pass to -in:file:template_pdb and the name in the header of the Grishin formatted alignment have to match. … or rather, it’s the first five characters which have to match. (The five characters are typically the 4-character PDB code and the 1 character chain ID.) Since you have only a 4 character name (I’m assuming “3vvt.pdb”, the ‘”.” is included in the matching, and you need to have it be present in the Grishin file — try making  the Grishin header contain the full name (without the path) of the PDB file you’re using. That should work in all cases.

[Author]

Posts