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<p>Good afternoon, <br>
</p>
<p>I contact you as I would really appreciate your help. I have a MD
trajectory which I have processed into Clusters with the Analysis
... Cluster tool. I have saved the resulting file with the members
and the representative frame, but now I would like to save those
representative frames in separate PDB files. This process is
extremely tedious if manually done, so I have tried to perform a
script:</p>
<p><br>
</p>
<p>with
open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt",
"r") as f:<br>
lines=f.readlines()<br>
cluster_number = 1<br>
for i in range(len(lines)):<br>
frame = i<br>
if mdInfo["frame number"] == frame:<br>
name =
"/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" +
str(cluster_number)<br>
runCommand('write format pdb 0 $name)</p>
<p><br>
</p>
<p>which would be run in the "Per-frame Commands", in order to 1)
encounter the frames of the cluster and 2) save each frame in a
PDB file, correctly numbered.</p>
<p><br>
</p>
<p>However, this script is not working, and I would greatly thank
any help you could provide me with.</p>
<p><br>
</p>
<p>Lorena.<br>
</p>
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<td style="width:370px;vertical-align:top;font-family:arial;font-size:12px;line-height:18px;" width="370" valign="top">
<span style="font-size:14px;font-weight:bold;color:#A54B04;">Lorena
Roldán Martín</span><br>
<b>PhD Student in Bioinformatics</b><br>
<br>
Departament de Química<br>
Unitat de Química Física<br>
<br>
Campus de la UAB · 08193 Bellaterra<br>
(Cerdanyola del Vallès) · Barcelona · Spain<br>
<br>
+34 690799431<br>
<a style="color:#A54B04;" href="http://www.uab.cat" ?="">www.uab.cat</a><br>
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<a href="https://orcid.org/0000-0002-6902-8285"><img max-width="40" src="https://www.uab.cat/vcard/ixs-id.png" width="40" height="40"></a><a href="https://www.linkedin.com/in/lorena-roldan-biomedica/"><img max-width="40" src="https://www.uab.cat/vcard/ixs-lin.png" width="40" height="40"></a>
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