how to prevent concatenation of protein chains in EOM

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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tomas
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how to prevent concatenation of protein chains in EOM

#1 Post by tomas » 2013.09.02 15:00

Working with protein complex made of several protein subunits:
the EOM output model is always concatenated (the C-terminus of subunit #n is always very close to N-terminus of the subunit #n+1)...

It is possible to prevent this concatenation and to force the EOM handle the domains as independent units?

Thank you,
Regards Tomas

Alex
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Re: how to prevent concatenation of protein chains in EOM

#2 Post by Alex » 2013.09.04 19:23

i think it is possible for now to work with multichain systems in eom only if it is homooligomer. there are workaround which have been
discussed earlier in this forum.

HTH, Alex

tomas
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Posts: 11
Joined: 2013.08.29 14:20

Re: how to prevent concatenation of protein chains in EOM

#3 Post by tomas » 2013.09.05 14:02

Hi Alex,
yes I found the topic with identical problem:
http://www.saxier.org/forum/viewtopic.p ... m+multiple
but without the advice how to solve this, just:
"With EOM 2.0 you can do that."
But how to do that?
Thank you,
Tomas

Alex
Active member
Posts: 692
Joined: 2007.08.09 21:10
Location: Planet Earth

Re: how to prevent concatenation of protein chains in EOM

#4 Post by Alex » 2013.09.05 14:35

Hi Tomas

Basically, if I were you - I would try to create a custom pool. This thread can be helpful:
http://www.saxier.org/forum/viewtopic.p ... aset#p4360

In a nutshell: you could split your multioligomer complex into single chains and generate missing parts using RaNCH for example, then
combine PDBs into different complex files (you might also want to do a clash check with, e.g. phenix.clashscore or similar).
Then you can use filtered pool as a custom pool in EOM.

HTH,
Alex

tomas wrote:Hi Alex,
yes I found the topic with identical problem:
http://www.saxier.org/forum/viewtopic.p ... m+multiple
but without the advice how to solve this, just:
"With EOM 2.0 you can do that."
But how to do that?
Thank you,
Tomas

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