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Structure prediction

Why there are two outputs using pmut_scan_parallel.linuxgccrelease with a mutant list file?

Category: 
Structure prediction

Dear friends,
I am using pmut_scan_parallel.linuxgccrelease to mutate a residue with a mutant list file. There are two PDB outputs for the point mutant. The two outputs are of slight difference at the mutated region. Can I ask why there are two outputs, and which one should I choose?

The original PDB and two outputs are attached.

Post Situation: 

ignore loops on threading

Category: 
Structure prediction

Hi there,
Is there any way to ignore some loops on threading? I'm trying to build a model based in a template which is about 30% identical to the query sequence. The sequence has lots of loops ranging from few aa to 80 aa. I was wondering if would be possible to ignore the biggest loop(s) at first and loopmodel them in a separate protocol.
Looks like the some loops are not closing so as the program finishes without build any model.
Perhaps someone could suggest a better approach.
Best,
Fred

Post Situation: 

Got error when running minirosetta.linuxgccrelease on cluster but fine on Ubuntu

Category: 
Structure prediction

Dear friends,
I am trying to run minirosetta.linuxgccrelease on our cluster.

I got the following message at the end of the log file:

[ERROR] EXCN_utility_exit has been thrown from: src/core/fragment/FragmentIO.cc line: 233
ERROR: ERROR: FragmentIO: could not open file $HOME/Scratch/20141110_HC_minirosetta/input/aaC226S_HC09_05.200_v1_3

This problem seems to be Rosetta specific and not relate to the cluster. However, I do not think there is anything wrong with "aaC226S_HC09_05.200_v1_3" and it works fine on my Ubuntu.

Post Situation: 

Run PackRotamersMover on specified rotamer set

Category: 
Structure prediction

Hi,

I would like to run PackRotamersMover to pack on a rotamer set which I specify. It looks like the setup code calls core::pack::pack_rotamers_setup() which builds the Dunbrack rotamer library. I'm guessing such functionality is not supported, maybe there is another mover which provides it?

Jason

Post Situation: 

Rotamers used in fixbb

Category: 
Structure prediction

Dear friends,
I am trying to use fixbb to replace some amino acid residues from a template PDB into my own sequence.

Can I ask
1) Is "-dun10" the latest rotamer database? (How can I know if it is the latest?)
2) Do I need to add additional flags (e.g. -ex1, -ex2, -ex3, -ex4) or they have been set by default?

Basically, I do not have particular requirement for the structure. So I am wondering if all the flags have been set by default?

Post Situation: 

If "clustering.py" can be used for PDBs contain two chains?

Category: 
Structure prediction

Dear friends,
Can I ask if "clustering.py" can be used for PDBs contain two chains? It works fine if there is only one chain in the PDB. However, when it comes to PDBs of two chains, it seems that no PDB structures have been processed. The following are the inputs and outputs for processing PDBs with two chains. Thank you very much.

Yours sincerely
Cheng

Post Situation: 

Get nchi for heavy atoms

Category: 
Structure prediction

Hi,

Is there a way to get the number of dihedral angles excluding the trailing hydrogen when it exists? I can manually check the residue types and subtract 1 when necessary, but I was wondering if this is already stored in a member field of Pose with an accessor function?

Thanks,
Jason

Post Situation: 

How can I prevent coordinates shift when using "loopmodel.linuxgccrelease"?

Category: 
Structure prediction

Dear friends,
I would like to use "loopmodel.linuxgccrelease" to remodel an internal loop of my heavy chain (HC). It works all fine except one defect: there are some coordinates shift between the output and the input. As I will finally combine light chain (LC) structure and heavy chain (HC) structure into one PDB file, these coordinates change will make the distance between LC and HC not the same as before. Can I ask how to solve this?

The input PDB and out PDB as well as the options files are attached.

My command line is:

Post Situation: 

"Segmentation fault" for "minirosetta.linuxgccrelease"

Category: 
Structure prediction

Dear friends,
I got "Segmentation fault (core dumped)" after running "minirosetta.linuxgccrelease":

~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/minirosetta.linuxgccrelease @/home/lanselibai/Cheng/test/LC/in/comparative_model_LC.options -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database >& /home/lanselibai/Cheng/test/LC/comparative_model_LC.log &

As suggested to test it on a debug mode (https://www.rosettacommons.org/node/3526), I have tried:

Post Situation: 

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