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User:Wayne Decatur/1cts to 2cts (citrate synthase) morph methods
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MORPH
First I removed model numbers from 1cts and 2cts and tried submitting to Yale Morph 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, 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:
- 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 PDB Goodies. It didn't matter that PDB Goodies ignored and left out the heteroatoms because the Morph Server does too.
- Then I each of those two produced files subsequently to the Yale Morph Server 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 renumbered the models from 0 through 11 to 1 to 12 so they'd work with Jmol.
- I added back the citrate and Acetyl-COA to
