{% extends "index.html" %} {% block indexuniq %} {% endblock %} {% block header %} Aggrescan3D: {{info['project_name']}} {% endblock %} {% block body %}
Settings
Change the job status manually
Statuses done and error mean the program will no longer automatically try to guess what the status is. Set to running if you wish for the program to guess the actual status.
Done Error Running
Rerun this job
Delete the log and start the job again with the same settings and in the same working directory
Rerun this job
Delete this job
If you no longer need the data or just don't want this project to populate the queue page simply delete it.
Remove from database Remove and delete files

Project name: {{info['project_name']}}

Status: {{info['status_color']|safe}}

Started: {{info['started']}}
{% if info['status'] == 'running' %} {% endif %}
Settings
{% if info['mutate']==1 %} {% endif %}
Working directory {{info['working_dir']|safe}}
Chain sequence(s) {{info['chain_sequence']|safe}}
Selected Chain(s) {{",".join(info['chains'])}}
Distance of aggregation {{info['distance']}} Å
FoldX usage {{info['foldx']}}
Dynamic mode {% if info['dynamic']==1 %} Yes {% else %} No {% endif %}
Automated mutations {% if info['auto_mutation_used'] %} Yes {% else %} No {% endif %}
Mutated residues {{ ",".join(info['mutation'].values()) }}
Energy difference between WT (input) and mutated protein (by FoldX) {{info['mutt_energy_diff']}} kcal/mol {% if info['mutt_energy_diff']|float > 1.0 %}

CAUTION: Your mutation/s can destabilize the protein structure

{% endif %}

Simulation's log

{% if info['status'] == 'done' %}
Show buried residues

Minimal score value
{{info['table']['min']|round(4)}}
Maximal score value
{{info['table']['max']|round(4)}}
Average score
{{info['table']['avg']|round(4)}}
Total score value
{{info['table']['sum']|round(4)}}

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

{% for row in info['table']['tab'] %} {% endfor %}
residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
{{row[0]}} {{row[1]}} {{row[2]}} {{row[3]}} {% if row[2]+row[0] in info['mutation'].keys() %}mutated: {{info['mutation'][row[2]+row[0]]}}{%endif %}
View in 3Dmol
Play the video
{% if info['dynamic'] %}

CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, {{info['table']['avg']|round(4)}} in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

{% if info['model_files'] == 'ok' %}
{% for model in info['avg_scores'] %} {% endfor %}
Model
Average A3D Score
{{model.split(".")[0]}} {{info['avg_scores'][model]}} View in 3Dmol
 
{% else %}

Models were not found for this run. Use verbosity 2 or higher to save models when running Aggrescan3D from command line.

{% for model in info['avg_scores'] %} {% endfor %}
Model
Average A3D Score
{{model.split(".")[0]}} {{info['avg_scores'][model]}}
 
{% endif %}
{% endif %} {% if info['auto_mutation'] %}

Automated mutations analysis

In the automated mutations mode A3D analysis is performed on the provided protein and then residues are chosen based on their score as candidates for mutations and each of those is then mutated into glutamic acid, lysine, aspartic acid and arginine. In this tab one can see the energetic and aggregation effects that the mutations had.
The results are stored in your project's work directory ({{info['working_dir']|safe}}}). Results for each mutant are stored in files starting with the mutation code (for example {{info['autom_data'].keys()[0] + '.pdb' }}. A summary csv file can be found in the working dir under the name of Mutations_summary.csv.

{% if info['autom_data'].values()[0] %}
{% for mutation, data in info['autom_data'].iteritems() %} {% endfor %}
Mutant
Energetic effect
Score comparison
{{mutation}} {{data[0]}} {{data[2]}} View
 
{% else %} {% if info['autom_data'].keys()[0] == "Data missing" %}

Your working directory seems to be missing the Mutations_summary.csv file which contains data required by this tab to load. (perhaps the job failed or the files were deleted manually?)

{% endif %} {% if info['autom_data'].keys()[0] == "No mutants" %}

It seems that no suitable candidates for mutation were found. Please see the simualtion's log

{% endif %} {% endif %}
{% endif %} {% endif %}
{% endblock %} {% block below_js %} {% endblock %} // This will be usefull for online server usgage - download version of model snapshots // // var pic_counter = 0; // var old_basename = ''; // $("form#data").submit(function(e) { // e.preventDefault(); // pic_counter++; // var name = $( '#text' ).val() || "snapshot"; // console.log($( '#text' ).val()); // var basename = name.split("_")[0]; // if (old_basename == '') old_basename = basename; // else { // if (old_basename != basename) { // pic_counter = 1; // old_basename = basename; // } // } // var new_name = basename+"_"+pic_counter; // downloadURI(name+'.jpeg'); // $('#text').val(new_name); // }); // // function downloadURI(filename) { // var element = document.createElement('a'); // var pic_code = viewer_2.pngURI(); // element.setAttribute('href', decodeURIComponent(pic_code)); // element.setAttribute('download', filename); // // element.style.display = 'none'; // document.body.appendChild(element); // // element.click(); // // document.body.removeChild(element); // }