Comments (8)
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Hello Nathan!
I'm looking at 3DKT.
All the best.
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I tried processing 3DKT with options --with-ph=2.0 --ph-calc-method=propka
like you said. One problem (after working around some others) is that propka will run out of chain identifiers. In my fork of pdb2pqr I increased the number of possible chains to 96. However, the assembly of 3DKT has 120 chains. It would be possible to process it after combining some of the chains.
I tried uploading a PDB file with combined chains to the new pdb2pqr server but it failed with 413 Request Entity Too Large (size is 11MB).
Upload to the old server worked but failed with dG out of range (error disguised as "local variable 'pH_opt' referenced before assignment", see this possible fix)
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from apbs.
Dear all,
thanks for the input!
First I tried with the asymmetric unit, now I want to use the biological assembly. How do I proceed now? I didn't really get it, sorry. If I want to upload the biological assembly I rename it to e.g. 3dkt_ba.pdb and upload it. If I want to visualize the surface potential afterwards in Pymol, I still only see the asymmetric unit and its surface potential. I lose the informations about other states or the other parts of the capsid can't visualize them.
Thanks for the patience for me as a newbie and greetings!
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from apbs.
Oops. That check-in should have been assigned to another issue. Sorry for confusion.
from apbs.
Hey Nathan,
unfortunately not. :(
All the best.
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