User:Wayne Decatur/1cts to 2cts (citrate synthase) morph methods: Difference between revisions

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Line 99: Line 99:
write COORDS PDB "extractcitrateforchainAformodel4.pdb";
write COORDS PDB "extractcitrateforchainAformodel4.pdb";


THEN repeated for chain B of MODELS 2-4:
NEXT repeated for model 5:
compare {1.1}{2.5} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainAformodel5.pdb";
 
NEXT repeated for model 6:
compare {1.1}{2.6} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainAformodel6.pdb";
 
THEN repeated for chain B of MODELS 2-6:
define citratebindingBchain 238,242,273,274,329,401 and :B;
define citratebindingBchain 238,242,273,274,329,401 and :B;
compare {1.1}{2.2} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
compare {1.1}{2.2} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
Line 118: Line 130:
write COORDS PDB "extractcitrateforchainBformodel4.pdb";
write COORDS PDB "extractcitrateforchainBformodel4.pdb";


NOW FOR frames closer to 2cts orientation for citrate:
NEXT repeated for model 5:
compare {1.1}{2.5} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainBformodel5.pdb";
 
NEXT repeated for model 6:
compare {1.1}{2.6} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainBformodel6.pdb";
 
NOW FOR frames (7-11) closer to 2cts orientation for citrate:
loaded 2ctsAB,pdb WHERE I HAD MADE PREVIOUSLY THE TWO CHAINS HAVE DIFFERENT DESIGNATIONS AS 2cts HAS AS BOTH A
loaded 2ctsAB,pdb WHERE I HAD MADE PREVIOUSLY THE TWO CHAINS HAVE DIFFERENT DESIGNATIONS AS 2cts HAS AS BOTH A


Line 124: Line 148:
THEN
THEN
define citratebindingAchain 238,242,273,274,329,401 and :A;
define citratebindingAchain 238,242,273,274,329,401 and :A;
compare {1.1}{2.5} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
compare {1.1}{2.7} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainAformodel7.pdb";
 
NEXT repeated for model 8:
compare {1.1}{2.8} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainAformodel8.pdb";
 
NEXT repeated for model 9:
compare {1.1}{2.9} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;  
select 1.1;  
write COORDS PDB "extractcitrateforchainAformodel5.pdb";
write COORDS PDB "extractcitrateforchainAformodel9.pdb";


NEXT repeated for model 6:
NEXT repeated for model 10:
compare {1.1}{2.6} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
compare {1.1}{2.10} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;  
select 1.1;  
write COORDS PDB "extractcitrateforchainAformodel6.pdb";
write COORDS PDB "extractcitrateforchainAformodel10.pdb";


NEXT repeated for model 7:
NEXT repeated for model 11:
compare {1.1}{2.7} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
compare {1.1}{2.11} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;  
select 1.1;  
write COORDS PDB "extractcitrateforchainAformodel7.pdb";
write COORDS PDB "extractcitrateforchainAformodel11.pdb";


THEN repeated for chain B of MODELS 5-7:
THEN repeated for chain B of MODELS 5-7:
define citratebindingBchain 238,242,273,274,329,401 and :B;
define citratebindingBchain 238,242,273,274,329,401 and :B;
compare {1.1}{2.5} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
compare {1.1}{2.7} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainBformodel7.pdb";
 
NEXT repeated for model 8:
compare {1.1}{2.8} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainBformodel8.pdb";
 
NEXT repeated for model 9:
compare {1.1}{2.9} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;  
select 1.1;  
write COORDS PDB "extractcitrateforchainBformodel5.pdb";
write COORDS PDB "extractcitrateforchainBformodel9.pdb";


NEXT repeated for model 6:
NEXT repeated for model 10:
compare {1.1}{2.6} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
compare {1.1}{2.10} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;  
select 1.1;  
write COORDS PDB "extractcitrateforchainBformodel6.pdb";
write COORDS PDB "extractcitrateforchainBformodel10.pdb";


NEXT repeated for model 7:
NEXT repeated for model 11:
compare {1.1}{2.7} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
compare {1.1}{2.11} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;  
select 1.1;  
write COORDS PDB "extractcitrateforchainBformodel7.pdb";
write COORDS PDB "extractcitrateforchainBformodel11.pdb";


*Opened file " 1ctsTO2cts.pdb " and saved as "1ctsTO2ctsCITRATEallframes.pdb" and then opened the files for chain A and B successively and copied and then pasted each of the citrates for the appropriate chain chain in the proper model in the "1ctsTO2ctsCITRATEallframes.pdb" file.
*Opened file " 1ctsTO2cts.pdb " and saved as "1ctsTO2ctsCITRATEallframes.pdb" and then opened the files for chain A and B successively and copied and then pasted each of the citrates for the appropriate chain chain in the proper model in the "1ctsTO2ctsCITRATEallframes.pdb" file.
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