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Results tagged with protein-structure
Search options questions only
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user 5180
The 3-D structure of a protein in space. It can refer to secondary structures, such as alpha helices or beta sheets, or the 3-D coordinates of the atoms making up a protein.
1
vote
2
answers
243
views
DMPfold error while running protein structure prediction
I am using DMPfold to predict protein structure of a 382 residue protein sequence. All goes wel, and even the files are produced but during the "seq2maps.csh", I get this error in between:
Running PS …
- 257
2
votes
1
answer
54
views
DMPfold: is it suitable to get 5000 models to compare with rosetta
I ran this command for 10 iteraions and 500 models.
run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./dmpfold-lysin 10 500 &> dmpfold-log.log
I am looking to generate 5000 dmpfold models to …
- 257
0
votes
2
answers
68
views
Can DMPfold and I-Tasser work well for de novo structure prediction of 1135 amino acid long ...
I am trying to perform de novo structure prediction of a 1135 long protein sequence; can DMPfold and I-Tasser work well for de novo structure prediction of 1135 amino acid long sequence?
- 257
1
vote
1
answer
31
views
A program "PSICOV" "stopped" from a few days on Ubuntu 18.04?
I am running dmpfold, "seq2maps.sh" and from a few days the program is at the "PSICOV" stage:
psicov -z 15 -o -d 0.03 tail-fiber-sequence.aln
"ps aux" gives me this:
daniel 26693 490 2.5 254 …
- 257
0
votes
1
answer
38
views
DMPfold: Understand the run of DMPfold "run_dmpfold.sh"?
I ran dmpfold using this command:
run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./dmpfold-lysin 10 500 &> dmpfold-log.log
It produced files like this:
sequence_sub_embed_1.pdb ..... sequ …
- 257
0
votes
1
answer
15
views
DMPfold: number of models produced using "10 500" feature in "run_dmpfold.sh"?
I ran this command:
run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./folder 10 500
From my previous discussion, I understand that I should run with default "run_dmpfold.sh" parameters i.e …
- 257
1
vote
1
answer
133
views
Rosetta ab initio run gives 0.00 RMSD for generated 2000 models? (run still in progress)
I am running rosetta ab initio prediction using the command line:
"mpiexec -np 16 /main/source/bin/AbinitioRelax.mpi.linuxgccrelease -database /main/database/ @options -mpi_tracer_to_file log > log1. …
- 257
2
votes
2
answers
101
views
Dmpfold error "No such file or directory: 'best_qdope.pdb'" when running "run_dmpfold.sh"?
I am running DMPfold, "seq2maps.sh" ran successfully, but whrn running "run_dmpfold.sh", it gives me this error:
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG I …
- 257
2
votes
1
answer
59
views
What does final generated models with TM-score of DMPfold signify in "sequence.ema.txt" file?
So, my runs have finished and got 5 final models. I predicted TM-score of one model to understand the result. The output of "predict-tmscore.sh" for "final_1.pdb" is:
1 models read from PDB file
1 mo …
- 257
3
votes
1
answer
111
views
How many models should be generated by rosetta for denovo protein structure prediction?
How many models should be generated by rosetta for de novo protein structure prediction of a 382 long sequence? In the tutorial, it says 50,000 models but practically it takes a lot of time (weeks) to …
- 257
1
vote
2
answers
70
views
Protein model quality assessment
How do I perform protein model quality assessment?
I will obtain predicted structures from DMPfold, I-Tasser, and Rosetta, what should be the next approach to select a structure from among this set o …
- 257