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

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Related to this work, it was suggested a morph like this one keep citrate in all the models (frames) since it is bound at both open and closed state. Because the morph server drops out heteroatoms, adding citrate to each frame, especially each monomer of the dimer, is not trivial and so I hadn't done. However, if I determine what residues are closest to citrate at each state and use the Jmol compare command focused only on those residues to match the open form to the first few frames of the morph and the same with the closed form for the last few frames. I should be able to save a file with the adjust coordinates and move citrate into the full morph of the appropriate frame. I would need to do a pass for each monomer. This should work better than just calculating a linear interpolation for each atom with the distance moved along a straight line divided among the number of frames currently in the animation (using Python) of the citrate atoms between the open and closed form as there may be some twisting and rotating of the citrate along the way that the straight line calculation for each atom wold not accommodate.
Related to this work, it was suggested a morph like this one keep citrate in all the models (frames) since it is bound at both open and closed state. Because the morph server drops out heteroatoms, adding citrate to each frame, especially each monomer of the dimer, is not trivial and so I hadn't done. However, if I determine what residues are closest to citrate at each state and use the Jmol compare command focused only on those residues to match the open form to the first few frames of the morph and the same with the closed form for the last few frames. I should be able to save a file with the adjust coordinates and move citrate into the full morph of the appropriate frame. I would need to do a pass for each monomer. This should work better than just calculating a linear interpolation (maybe more clearly stated as transposition or translation?) for each atom with the distance moved along a straight line divided among the number of frames currently in the animation (using Python) of the citrate atoms between the open and closed form as there may be some twisting and rotating of the citrate along the way that the straight line calculation for each atom wold not accommodate.
* Will be doing this with morph file with all atoms ("1ctsTO2cts.pdb"), because work related to this used that file to show all atoms.
* Will be doing this with morph file with all atoms ("&nbsp;1ctsTO2cts.pdb"), because work related to this used that file to show all atoms.
* In Jmol determined residues close to citrate in 1cts:
select within (4.5, [CIT]);
show residues;
YIELDS
[HIS]238:A
[ASN]242:A
[LEU]273:A
[HIS]274:A
[ARG]329:A
[ARG]401:A
 
 
select within (5.0, [CIT]);
show residues;
YIELDS
[HIS]238:A
[ASN]242:A
[LEU]273:A
[HIS]274:A
[ARG]329:A
[PHE]397:A
[ARG]401:A
 
LIST LONGER FOR 2cts but all same residues overlap too so probably can use same list for each to make easier.
 
TO MAKE IT EASIER TO DO FOR EACH MONOMER SINCE EACH MOVE RELATIVE OTHER AND WANT TO NOT RESTRICT TO BEST FIT WITH DIMER:
loaded 1ctsAB,pdb WHERE I HAD MADE PREVIOUSLY THE TWO CHAINS HAVE DIFFERENT DESIGNATIONS AS 1cts HAS AS BOTH A
 
THEN OPEN AS APPEND 1ctsTO2cts.pdb
THEN
define citratebindingAchain 238,242,273,274,329,401 and :A;
compare {1.1}{2.2} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainAformodel2.pdb";
 
NEXT repeated for model 3:
compare {1.1}{2.3} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainAformodel3.pdb";
 
NEXT repeated for model 4:
compare {1.1}{2.4} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainAformodel4.pdb";
 
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;
compare {1.1}{2.2} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainBformodel2.pdb";
 
NEXT repeated for model 3:
compare {1.1}{2.3} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainBformodel3.pdb";
 
NEXT repeated for model 4:
compare {1.1}{2.4} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainBformodel4.pdb";
 
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
 
THEN OPEN AS APPEND 1ctsTO2cts.pdb
THEN
define citratebindingAchain 238,242,273,274,329,401 and :A;
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:
select 1.1;
write COORDS PDB "extractcitrateforchainAformodel9.pdb";
 
NEXT repeated for model 10:
compare {1.1}{2.10} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainAformodel10.pdb";
 
NEXT repeated for model 11:
compare {1.1}{2.11} SUBSET {*.CA} ATOMS {citratebindingAchain}{citratebindingAchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainAformodel11.pdb";
 
THEN repeated for chain B of MODELS 5-7:
define citratebindingBchain 238,242,273,274,329,401 and :B;
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:
select 1.1;
write COORDS PDB "extractcitrateforchainBformodel9.pdb";
 
NEXT repeated for model 10:
compare {1.1}{2.10} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainBformodel10.pdb";
 
NEXT repeated for model 11:
compare {1.1}{2.11} SUBSET {*.CA} ATOMS {citratebindingBchain}{citratebindingBchain} rotate translate;
WAIT AND LET FINISH MOVING AND THEN ISSUE THESE COMMANDS:
select 1.1;
write COORDS PDB "extractcitrateforchainBformodel11.pdb";
 
*Opened file "&nbsp;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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