User:Wayne Decatur/1cts to 2cts (citrate synthase) morph methods: Difference between revisions
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==MORPH== | ==MORPH== | ||
First I removed model numbers from [[1cts]] and [[2cts]] and tried submitting to Yale Morph [http://molmovdb.mbb.yale.edu/cgi-bin/beta.cgi beta server] for multichains. It turns out it just did one chain of a for each and not the dimer. So I kept those files (could be of use for showing the changes in a single chain on the citrate synthase page), renumbered the models from 0 through 7 to 1 through 8 '''(SO THEY WORK PROPERLY WITH JMOL)''', and then added back the ligands (citric acid and C to chain 8 by using MagicFit in Swiss PDB | First I removed model numbers from [[1cts]] and [[2cts]] and tried submitting to Yale Morph [http://molmovdb.mbb.yale.edu/cgi-bin/beta.cgi beta server] for multichains. It turns out it just did one chain of a for each and not the dimer. So I kept those files (could be of use for showing the changes in a single chain on the citrate synthase page), renumbered the models from 0 through 7 to 1 through 8 '''(SO THEY WORK PROPERLY WITH JMOL)''', and then added back the ligands (citric acid and C to chain 8 by using MagicFit in Swiss-PDB Viewer like described in the 3kg2 morph methods. Turns out since citrc acid in both start and end models, that I should have fitted that part in to all models. However, getting things done for dimer is more important. | ||
To do dimer: | To do dimer: | ||
* I removed references to model numbers from 1cts and 2cts. | * I removed references to model numbers from 1cts and 2cts. | ||
* Then using the second set of chain A in each PDB file, I changed the chain identifier to B for that part using part of the file in [http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/ PDB Goodies]. It didn't matter that PDB Goodies ignored and left out the heteroatoms because the Morph Server does too. I ended up needing to add the ligands back later to the A and B chain files to do fitting to get ligands back, and second set of ligands I just set to chain B by hand since not worth setting up my Python scripts just for a few lines. | * Then using the second set of chain A in each PDB file, I changed the chain identifier to B for that part using part of the file in [http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/ PDB Goodies]. It didn't matter that PDB Goodies ignored and left out the heteroatoms because the Morph Server does too. I ended up needing to add the ligands back later to the A and B chain files to do fitting with SWISS-PDB VIEWER to get ligands back, and second set of ligands I just set to chain B by hand since not worth setting up my Python scripts just for a few lines. | ||
* Then I each of those two produced files subsequently to the Yale Morph Server [http://molmovdb.mbb.yale.edu/cgi-bin/beta.cgi Beta Server] and got the result quickly. | * Then I each of those two produced files subsequently to the Yale Morph Server [http://molmovdb.mbb.yale.edu/cgi-bin/beta.cgi Beta Server] and got the result quickly. | ||
* I downloaded the produced multi-model file by clicking on the Jmol icon in the corner and selecting view movie.pdb.gz from the menu and unzipped the file. | * I downloaded the produced multi-model file by clicking on the Jmol icon in the corner and selecting view movie.pdb.gz from the menu and unzipped the file. | ||
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* Gzipped and Uploaded as [[Image:1ctsTO2cts.pdb.gz]] | * Gzipped and Uploaded as [[Image:1ctsTO2cts.pdb.gz]] | ||
<Structure load='1ctsTO2cts.pdb.gz' size='500' frame='true' align='right' scene='User:Wayne_Decatur/1cts_to_2cts_(citrate_synthase)_morph_methods/1ctsto2ctsmorph/ | <Structure load='1ctsTO2cts.pdb.gz' size='500' frame='true' align='right' scene='User:Wayne_Decatur/1cts_to_2cts_(citrate_synthase)_morph_methods/1ctsto2ctsmorph/4' caption='open to closed morph' /> | ||
