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PostPosted: Sun Sep 15, 2013 3:59 pm 
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Greetings -

I have a file downloaded from Li et al (2008) Proteins 71:938–949 supplemental materials in which the authors modeled CYP2J2 using var. modeling platforms. I would like to take this modeled protein and dock a substrate using AUTODOCK but the problem I am facing is that the file only appears to have xyz coordinates - I've had no luck opening it in any viewer. The file format is:
Code:
REMARK Accelrys ViewerPro PDB file
ATOM 1 N PRO 44 26.718 16.691 29.230 0.00 0.00
ATOM 2 CD PRO 44 26.149 18.006 28.898 0.00 0.00
ATOM 3 CG PRO 44 27.329 18.892 28.519 0.00 0.00
ATOM 4 CB PRO 44 28.258 17.911 27.796 0.00 0.00
ATOM 5 CA PRO 44 27.794 16.504 28.231 0.00 0.00
...
...
...
...
ATOM 3767 NE2 GLN 501 71.420 53.765 28.558 0.00 0.00
ATOM 3768 C GLN 501 69.046 57.494 30.448 0.00 0.00
ATOM 3769 O GLN 501 68.749 58.052 29.367 0.00 0.00
ATOM 3770 OXT GLN 501 68.875 58.053 31.558 0.00 0.00
TER
<EOF>

Relative to a PDB file there are no connection lines. I suppose one could format the file to meet *.xyz formatting standards which might then be convertable to a PDB file.

I could send an email to the authors (in China) but I'd rather not do that if possible. Also I do not have $300 for ViewerPro which I assume could handle this.

Any ideas? Thanks in advance for any thoughts on how you might proceed with this.


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PostPosted: Wed Nov 13, 2013 2:56 am 
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If I understand your question correctly, you should be able to use Discovery Studio 3.5 to open your .ter file, and then save it as a .pdb file.

It's free software,

http://accelrys.com/products/discovery- ... s-350.html

Let me know if that helps.


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