tutorials:eccb_t2_fundi

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### FunDi

Installation:

Download it from https://github.com/dgaston/FunDi
=> ZIP buttom

<code>
unzip dgaston-FunDi-229c4d6.zip
cd dgaston-FunDi-229c4d6/
unzip qmmraxml.zip
export PATH=$PATH:qmmraxml  # Or mv qmmraxml/qmmraxmlHPC to a PATH folder
</code>

if not working, you may need to recompile qmmraxmlHPC

<code>
unzip dgaston-FunDi-229c4d6.zip
cd dgaston-FunDi-229c4d6/
unzip qmmraxml.zip
cd qmmraxml
make  clean   # remove all files
make          # compile qmmraxmlHPC
cd ..
export PATH=$PATH:qmmraxml  # or move  qmmraxmlHPC in a path folder.
</code>

FunDi needs PERL release 5.10 or higher (maybe with threads enabled).

Execution:
<code>
perl FunDi.pl -a GAPDH_alignment.phy -o gapdh_subtree -m LG -s gapdh_subtree.def -P qmmraxml -r 4 -t gapdh.tre
</code>

=> Results are in file FunDi_Posterior_Scores.txt

You can load it in your spreadsheet (tab separated, activate special detection of numbers).
The numbering of sites starts from 0.
Sites with a posterior probality P(FD) with 0.50 or more could be interesting.

In particular:
sites 38 (=39 in Jalview) (=34 in the structure 2PKQ)
sites 193 (=194 in Jalview) (=188 in the structure 2PKQ)
sites 195 (=196 in Jalview) (=191 in the structure 2PKQ)

Open PyMol and load protein 2PKQ
<code>
Plugins-> PDB Loader Service 
</code>

<code>
all->S->Show->as->Cartoon
all->C->Color by->chain
</code>

In the PyMol command line:
<code>
select ImportantSites, resi 34+188+191 
</code>

<code>
(ImportantSites)->S->Show->Spheres
(ImportantSites)->C->Color by->chain
</code>

Trace: • eccb_t2_diverge • motif • grath • beta_sheet • test • eccb_t2_fundi • four_helix_bundle • alpha_beta_plait • superfamily_naming_tutorial

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