[Chimera-users] Clustering saving PDB

[Lorena Roldán]

Good afternoon,

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:


with 
open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", 
"r") as f:
     lines=f.readlines()
     cluster_number = 1
     for i in range(len(lines)):
         frame = i
         if mdInfo["frame number"] == frame:
             name = 
"/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + 
str(cluster_number)
             runCommand('write format pdb 0 $name)


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.


However, this script is not working, and I would greatly thank any help 
you could provide me with.


Lorena.

-- 
<http://www.uab.cat> 	Lorena Roldán Martín
*PhD Student in Bioinformatics*

Departament de Química
Unitat de Química Física

Campus de la UAB · 08193 Bellaterra
(Cerdanyola del Vallès) · Barcelona · Spain

+34 690799431
www.uab.cat <http://www.uab.cat>


	<https://orcid.org/0000-0002-6902-8285><https://www.linkedin.com/in/lorena-roldan-biomedica/>

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