<p>The <code>sequence_n.pdb</code> files are temporary and are combined into an <code>ensemble.i.pdb</code> file after each iteration <code>i</code>. That file has many structures in. After the run is complete there will be a <code>final_1.pdb</code> file. Don't worry about the cluster files. If you are interested in what they do, consult the <code>run_dmpfold.sh</code> script and see what it is doing line by line.</p>

<p>As I have said multiple times elsewhere, you should run the script with default parameters and let it run <em>to completion</em>. Then use the <code>final_1.pdb</code> and any other <code>final_*.pdb</code> files as the output. If you want more structures, use the <code>ensemble.i.pdb</code> files.</p>

CC BY-SA 4.0
2019-09-17T11:13:42.957Z
2019-09-17T11:13:42.957Z
jgreener
<p>I ran this command:</p>

<pre><code>run_dmpfold.sh sequence.fasta sequence.21c sequence.map ./folder 10 500 
</code></pre>

<p>From my previous discussion, I understand that I should run with default "run_dmpfold.sh" parameters i.e. <code>3 50</code>; however, since I have already run the <code>10 500</code> I have some questions.</p>

<p>I see that after generating "sequence_1.pdb to sequence_500.pdb" files, these files are no more in the folder and, now I see "ensemble_1.pdb". 
Will there be more ensemble files like "ensemble_500.pdb" and "sequence_n.pdb" files? I mean when can I expect "final_1.pdb' file? Also, I see files like "CLUSTERS_001.pdb".</p>

<protein-structure>
DMPfold: number of models produced using "10 500" feature in "run_dmpfold.sh"?
# DMPfold: number of models produced using "10 500" feature in "run_dmpfold.sh"?

(Asked by: username_0 on 2019-09-17)

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. 3 50; however, since I have already run the 10 500 I have some questions.
I see that after generating "sequence_1.pdb to sequence_500.pdb" files, these files are no more in the folder and, now I see "ensemble_1.pdb". 
Will there be more ensemble files like "ensemble_500.pdb" and "sequence_n.pdb" files? I mean when can I expect "final_1.pdb' file? Also, I see files like "CLUSTERS_001.pdb".

**Tags:** protein-structure

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## 1 answers

### Answer by username_1 on 2019-09-17. Score: 0 | Accepted answer

The `sequence_n.pdb` files are temporary and are combined into an `ensemble.i.pdb` file after each iteration `i`. That file has many structures in. After the run is complete there will be a `final_1.pdb` file. Don't worry about the cluster files. If you are interested in what they do, consult the `run_dmpfold.sh` script and see what it is doing line by line.

As I have said multiple times elsewhere, you should run the script with default parameters and let it run *to completion*. Then use the `final_1.pdb` and any other `final_*.pdb` files as the output. If you want more structures, use the `ensemble.i.pdb` files.


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