User:Wayne Decatur/1cts to 2cts (citrate synthase) morph methods
From Proteopedia
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 (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:
- 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. 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. (For 3cts,5cts, and 6cts biological files, later I did just with word processing using search for A with space in front and behind because didn't need for morph and wanted all hetero atoms. Removed eferences to model numbers from thes3 3 files 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 files using the ones I used to generate the files plus the ligands added and labeled (see second step above).
- Gzipped and Uploaded as Image:1ctsTO2cts.pdb.gz
- However, I realized after uploading it and making a scene that I forgot to reduce it to just the alpha carbons first using alphac.exe (2nd edition). So I did that, gzipped, and uploaded as Image:CA1ctsTO2cts.pdb.gz .
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These two morphs are used on the Citrate Synthase page.
On the Morphs page, I had at one time also used this:.
Testing code for the Morphs page:
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