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which alm for bunch ?

Posted: 2017.05.11 18:09
by gia75
Dear All,

I have a protein with long flexible n-term and c-term
which pdb should i take to calculate the .alm file for bunch ?
should i take the structure generated by pre-bunch or the original structure with n-term and c-term removed ?
sorry for the question but it is not clear to me (yet)

Thank you all

Re: which alm for bunch ?

Posted: 2017.05.12 13:35
by gia75
ps:
actually what i would like to do, is to input a starting conformation for my entire protein
and then let bunch move the flexible regions only
i understand that this is not the classical way of using bunch
is it possible to that ?

Thanks

Re: which alm for bunch ?

Posted: 2017.05.12 15:42
by Alex
you should take the original structure with n-term and c-term removed.

If it is that flexible (as you can see from comparative dimensionless Kratky plot), you better use EOM and let it output PDB files. This you
will get a large random pool with variable conformation of flexible parts.

HTH, Alex

Re: which alm for bunch ?

Posted: 2017.05.12 18:33
by gia75
Hi and thank you

the problem is that it is not that flexible...
the domain probably samples several different conformations while retaining its local secondary structure, more or less like a spring ;o)
how to model something like that ?

GIA

Re: which alm for bunch ?

Posted: 2017.05.12 18:50
by Alex
the problem is that it is not that flexible...

it's best to check dKratky plot preferably with reference folded/unfolded proteins.
Or have some additional evidence from CD spectra, for example.

Based on result, you can judge about level and regions of flexibility.

To me it sounded like that you have only flexible N-/C- terminus while the rest was more or less rigid.

BUNCH will assume rigid part stays the same and that there is a single conformation in solution.
EOM will assume rigid part stays the same and that there are multiple conformations in solution.
SREFLEX will assume rigid part may somewhat change and there is one/limited conformations in solution.

HTH, Alex