====================================================================================


((Chimeara commands))
=====================

log clear;	// clear the log
close session;	// close session

/bin/chimerax --nogui < ./Vimentin.bat

/bin/chimerax --nogui < ./Annexin_A2.bat



=====================

- dock prep
	Tools
	Structure Editing
	Dock Prep
	
- strip  hydrogens
	Select
	Chemistry
	Element
	H
	
	Action
	Atom/Bonds
	Delete		

open /home/rick/mabovsky/InI_Max/va_chimera/Vimentin.pdb;
dockprep #1;
select H;
delete atoms sel;	// hydrogen is default
delete bonds sel;	// hydrogen is default
save /home/rick/mabovsky/InI_Max/va_chimera/Vimentin_CMD.pdb relModel #1;



======================

- add hydrogens
	Tools
	Structure Editing
	Add Hydrogens

- add charges
	Tools
	Stucture Editing
	Add Charges

open /home/rick/mabovsky/InI_Max/va_chimera/Annexin_A2.pdb;
addh #1;
addcharge #1;
save /home/rick/mabovsky/InI_Max/va_chimera/Annexin_A2_CMD.pdb relModel #1;








((InI_Sets))
====================================================================================
      
 - move to folders where all decoys are.
 - copy "InI_Sets.jar" there
 - use one of below to run:
(development)           
    java -jar ./InI_Sets.jar . 24
(manually)              
    nohup java -jar ./InI_Sets.jar . 24 > set.out 2>&1 &
(srun to computer node) 
    srun --cpus-per-task 1 -o set.out -e set.err java -jar ./InI_Sets.jar . 24 &
    
Input: 
 - '.' is a path to folder 'full' of decoys
 - 24  is a number of decoys to us

Output:
Signature_4.txt // 4 is a max distance in 'A'
        
        




((Commands))
=========================================================================================
 


scp ./va_chimera.zip  mabovsky@ijcluster.uhnres.utoronto.ca:/home/mabovsky/PP_Docking/MEGADOCK/.
unzip va_chimera.zip




srun --cpus-per-task 20 --pty bash -i
cd /home/mabovsky/PP_Docking/MEGADOCK/va_chimera
../megadock-4.1.1/megadock -R Vimentin_chimera.pdb -L Annexin_A2_chimera.pdb -t 3 -N 10800

../megadock-4.1.1/decoygen Annexin_A2_chimera.1.pdb Annexin_A2_chimera.pdb Vimentin_chimera-Annexin_A2_chimera.out 1
cat Vimentin_chimera.pdb Annexin_A2_chimera.1.pdb > vim_ann.1.pdb

../megadock-4.1.1/decoygen Annexin_A2_chimera.2.pdb Annexin_A2_chimera.pdb Vimentin_chimera-Annexin_A2_chimera.out 2
cat Vimentin_chimera.pdb Annexin_A2_chimera.2.pdb > vim_ann.2.pdb

../megadock-4.1.1/decoygen Annexin_A2_chimera.3.pdb Annexin_A2_chimera.pdb Vimentin_chimera-Annexin_A2_chimera.out 3
cat Vimentin_chimera.pdb Annexin_A2_chimera.3.pdb > vim_ann.3.pdb

../megadock-4.1.1/decoygen Annexin_A2_chimera.4.pdb Annexin_A2_chimera.pdb Vimentin_chimera-Annexin_A2_chimera.out 4
cat Vimentin_chimera.pdb Annexin_A2_chimera.4.pdb > vim_ann.4.pdb

../megadock-4.1.1/decoygen Annexin_A2_chimera.5.pdb Annexin_A2_chimera.pdb Vimentin_chimera-Annexin_A2_chimera.out 5
cat Vimentin_chimera.pdb Annexin_A2_chimera.5.pdb > vim_ann.5.pdb

cd /home/mabovsky/PP_Docking/MEGADOCK/
zip -r va_chimera_done.zip va_chimera



cd /home/rick/mabovsky/InI_Max

scp mabovsky@ijcluster.uhnres.utoronto.ca:/home/mabovsky/PP_Docking/MEGADOCK/va_chimera_done.zip ./.
unzip va_chimera_done.zip






<_folders_xx-XX>
====================


scp ./_folders_3_test.zip  mabovsky@ijcluster.uhnres.utoronto.ca:/home/mabovsky/PP_Docking/MEGADOCK/run/.


unzip _folders_3_test.zip
cd _folders_3_test
chmod u+x master.sh
nohup ./master.sh > master.out 2>&1 &




scp ./_folders_i_200.zip mabovsky@ijcluster.uhnres.utoronto.ca:/home/mabovsky/PP_Docking/MEGADOCK/run/.


unzip _folders_i_200.zip
cd _folders_i_200
chmod u+x master.sh
nohup ./master.sh > master.out 2>&1 &


        
        




((InI_Delta))
=========================================================================================

cd run      # move to run folder

# create 2 files here:

    file = "i.txt"
        _folders_i_200_done/Signatures_4.0.txt

    file = "n.txt"
        _folders_ne_200_done/Signatures_4.0.txt
        _folders_ne_800_done/Signatures_4.0.txt

java -jar InI_Delta.jar        

# results are:

    I minus N
  ------------------------------
  CYS-OXT-N-ASN
  CYS-OXT-N-TRP
  GLY-OXT-CD2-TYR
  GLY-OXT-CG-ASN
  GLY-OXT-N-HIS
  ILE-OXT-C-TRP
  ILE-OXT-O-TRP
  LYS-OXT-OXT-GLU
  TRP-CD2-OXT-CYS
  TRP-CG-OXT-CYS
   >> lstIminusN.size() = 10