View source for CD task7 protocol

== Choosing structure ==

So, we decided to use 2O4H, since it has a bound substrate, low resolution and a listed pH value. 

 Apo-structure:       2O53 Resolution: 2,7,  R-free: 0,269, pH: 6.0, chains: A,B
 Holo-structure:      2O4H Resolution: 2,7,  R-free: 0,271, pH: 6.0, chains: A,B intermediate substrate analog: N-phosphonomethyl-L-aspartate
 Apo-structure:       2I3C Resolution: 2,8,  R-free: 0,243, pH: -  , chains: A,B
 Ensemble Refinement  2Q51 Resolution: 2,8,  R-free: 0,239, pH: -  , chains: A,B

For 2O4H, there are only missing residues at the N- and C-terminal ends, which can be neglected:
 REMARK 465 MISSING RESIDUES                                                     
 REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
 REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
 REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) 
 REMARK 465   M RES C SSSEQI                                                     
 REMARK 465   1 ALA A    -1                                                      
 REMARK 465   1 ILE A     0                                                      
 REMARK 465   1 ALA A     1                                                      
 REMARK 465   1 THR A     2                                                      
 REMARK 465   1 SER A     3                                                      
 REMARK 465   1 CYS A     4                                                      
 REMARK 465   1 HIS A     5                                                      
 REMARK 465   1 ILE A     6                                                      
 REMARK 465   1 ALA A     7                                                      
 REMARK 465   1 GLU A     8                                                      
 REMARK 465   1 CYS A   311                                                      
 REMARK 465   1 LEU A   312                                                      
 REMARK 465   1 HIS A   313

==Scwrl==

 #first nine residues are missing
 # read sequence
 line = open("./aspa_crop.fasta","r").readlines()[1]
 #make lower case
 seq = line.lower().strip("\n")
 print(line) 
 
 #(posi, orig aa, mut aa)
 muts = [(285, "e", "a","E285A"),(305,"a","e","A305E"),(123,"g","e","G123E"),(71,"r","h","R71H"),(71,"r","k","R71K"),(213,"k","e","K213E"),(278,"v","m","V278M"),(82,"m","t","M82T"), (235,"e","k","E235K"),(270,"i","t","I270T")]
 
 for mut in muts:
         #check if looking at correct residue
         if not seq[mut[0]-10] == mut[1]:
                 print mut, 'wrong residue match'
         else:
                 l = list(seq)
                 l[mut[0]-10] = mut[2].upper()
                 newSeq = "".join(l)
                 st = mut[3] + ".fasta"
                 outfile = open(st,"w")
 #               st = "> " + mut[3] + "\n"
 #               outfile.write(st)
                 outfile.write(newSeq)   
 
 callfile = open("./callSCWRL.sh","w") 
 
 for mut in muts:
         st = "/opt/SS12-Practical/scwrl4/Scwrl4 -i 2O4H_chainA.pdb -o " + mut[3] + "_scwrl.pdb" + " -s " + mut[3] + ".fasta\n"
         callfile.write(st) 
 
 /opt/SS12-Practical/scwrl4/Scwrl4 -i 2O4H_chainA.pdb -o E285A_scwrl.pdb -s E285A.fasta

==FoldX==

list.txt
 2O4H.pdb

individual_list.txt
 EA285A;
 AA305E;
 GA123E;
 RA71H;
 RA71K; 
 KA213E;
 VA278M;
 MA82T;
 EA235K;
 IA270T;

run.txt
 <TITLE>FOLDX_runscript;
 <JOBSTART>#;
 <PDBS>#;
 <BATCH>list.txt;
 <COMMANDS>FOLDX_commandfile;
 <BuildModel>#,individual_list.txt;
 <END>#;
 <OPTIONS>FOLDX_optionfile;
 <Temperature>298;
 <R>#;
 <pH>7;
 <IonStrength>0.050;
 <water>-CRYSTAL;
 <metal>-CRYSTAL;
 <VdWDesign>2;
 <OutPDB>true;
 <pdb_hydrogens>false;
 <complex_with_DNA> true; 
 <END>#;
 <JOBEND>#;
 <ENDFILE>#;

command
 /opt/SS12-Practical/foldx/FoldX.linux64 => choose 3 => run.txt

==Minimise==

We prepared the .pdb files with pymol (remove hydrogens, solvent)

 /opt/SS12-Practical/minimise/minimise E285A_scwrl_repair.pdb E285A_scwrl_min.pdb