<commit_before>
<h1>Help</h1>

<ul> 
<li>
<a id="email"><b>E-mail address</b></a>

<p>If an e-mail address is entered here, it will be used to notify you
when the job has completed. (Unlike older versions of ModLoop, the PDB file
is not emailed directly to you, but can be downloaded from this web site.).</p>
</li>

<li>
<a id="modkey"><b>MODELLER key</b></a>

<p>This server is freely available for academic users. The loop modeling
module is implemented in the MODELLER program, therefore you need to register
for a license of MODELLER. It can be done online and
automatically by accessing the
<a href="http://salilab.org/modeller/registration.html">MODELLER web site</a>.
The web site will email you a MODELLER key. You need to enter this license key
here in order to use this server.</p>
</li>

<li>
<a id="file"><b>Upload your file</b></a>

<p>The uploaded coordinate file must be a valid PDB format file. The loop region
to be modeled must be included in the coordinate file, since the amino acid
sequence and initial loop energy are derived from the PDB file. (You can give
the loop atoms dummy coordinates, but each atom must have different coordinates,
or you will get a 'Central bond too short' error from Modeller.)</p></li>

<li>
<a id="loop"><b>Select loop segment</b></a>

<p>The starting and ending residue positions and chain identifiers (if any)
should be specified here, separated by ":". One can specify several loop
segments, but the total number of residues involved in the loops must not
exceed 14. Only regular amino acids can be selected for loop modeling (i.e.
no non-standard residues such as ligands, DNA strands, etc.) although the
non-loop regions of your PDB <i>can</i> contain non-standard residues.
Please use the following syntax:</p>

<p>Example 1. one loop between residues 12 and 18 in chain B:</p>
<pre>12:B:18:B:</pre>

<p>Example 2. one loop between residues 15 and 22, no chain identifier,
another loop between residues 98 and 103 in chain B and one more residue, at
position 66 in chain C to be selected:</p>

<pre>fd00:c2b6:b24b:be67:2827:688d:e6a1:6a3b::
98:B:103:B:
66:C:66:C:
</pre>
</li>

<li>
<a id="name"><b>Name of the model</b></a>

<p>The name entered here is used to identify your job in the ModLoop
system.</p>
</li>

</ul>

<hr />

<h3><a id="errors">Common errors</a></h3>

<ul>
<li><b>'Central bond too short'</b>: this is usually caused by having two or
more atoms in your input PDB file with the same coordinates. (Tip: if you
don't know the original coordinates of your loop, specify dummy
coordinates, but don't put every atom at (0,0,0).)</li>

<li><b>'some selected residues have no topology'</b>: the loop modeling
protocol is only defined on standard amino acids. Thus, you can't select
residues for modeling which have no defined MODELLER topology, such as
DNA/RNA, metal ions, or ligands.</li>
</ul>

<commit_msg>Correct grammar.<commit_after>
<h1>Help</h1>

<ul> 
<li>
<a id="email"><b>E-mail address</b></a>

<p>If an e-mail address is entered here, it will be used to notify you
when the job has completed. (Unlike older versions of ModLoop, the PDB file
is not emailed directly to you, but can be downloaded from this web site.)</p>
</li>

<li>
<a id="modkey"><b>MODELLER key</b></a>

<p>This server is freely available for academic users. The loop modeling
module is implemented in the MODELLER program, therefore you need to register
for a license of MODELLER. It can be done online and
automatically by accessing the
<a href="http://salilab.org/modeller/registration.html">MODELLER web site</a>.
The web site will email you a MODELLER key. You need to enter this license key
here in order to use this server.</p>
</li>

<li>
<a id="file"><b>Upload your file</b></a>

<p>The uploaded coordinate file must be a valid PDB format file. The loop region
to be modeled must be included in the coordinate file, since the amino acid
sequence and initial loop energy are derived from the PDB file. (You can give
the loop atoms dummy coordinates, but each atom must have different coordinates,
or you will get a 'Central bond too short' error from Modeller.)</p></li>

<li>
<a id="loop"><b>Select loop segment</b></a>

<p>The starting and ending residue positions and chain identifiers (if any)
should be specified here, separated by ":". One can specify several loop
segments, but the total number of residues involved in the loops must not
exceed 14. Only regular amino acids can be selected for loop modeling (i.e.
no non-standard residues such as ligands, DNA strands, etc.) although the
non-loop regions of your PDB <i>can</i> contain non-standard residues.
Please use the following syntax:</p>

<p>Example 1. one loop between residues 12 and 18 in chain B:</p>
<pre>12:B:18:B:</pre>

<p>Example 2. one loop between residues 15 and 22, no chain identifier,
another loop between residues 98 and 103 in chain B and one more residue, at
position 66 in chain C to be selected:</p>

<pre>fd00:c2b6:b24b:be67:2827:688d:e6a1:6a3b::
98:B:103:B:
66:C:66:C:
</pre>
</li>

<li>
<a id="name"><b>Name of the model</b></a>

<p>The name entered here is used to identify your job in the ModLoop
system.</p>
</li>

</ul>

<hr />

<h3><a id="errors">Common errors</a></h3>

<ul>
<li><b>'Central bond too short'</b>: this is usually caused by having two or
more atoms in your input PDB file with the same coordinates. (Tip: if you
don't know the original coordinates of your loop, specify dummy
coordinates, but don't put every atom at (0,0,0).)</li>

<li><b>'some selected residues have no topology'</b>: the loop modeling
protocol is only defined on standard amino acids. Thus, you can't select
residues for modeling which have no defined MODELLER topology, such as
DNA/RNA, metal ions, or ligands.</li>
</ul>


{'fraction_non_alphanumeric': 0.10829573064908019, 'fraction_numerical': 0.020131898646303367, 'mean_word_length': 4.488571428571428, 'pattern_counts': {'":': 2, '<': 145, '<?xml version=': 0, '>': 145, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2520855', 'n_tokens_mistral': 1916, 'n_tokens_neox': 1772, 'n_words': 861}