User:Wayne Decatur/1cts to 2cts (citrate synthase) morph methods: Difference between revisions
mNo edit summary |
mNo edit summary |
||
| Line 17: | Line 17: | ||
<!-- <Structure load='1ctsTO2cts.pdb.gz' size='500' frame='true' align='right' scene='User:Wayne_Decatur/1cts_to_2cts_(citrate_synthase)_morph_methods/1ctsto2ctsmorph/5' caption='open to closed morph' /> --> | <!-- <Structure load='1ctsTO2cts.pdb.gz' size='500' frame='true' align='right' scene='User:Wayne_Decatur/1cts_to_2cts_(citrate_synthase)_morph_methods/1ctsto2ctsmorph/5' caption='open to closed morph' /> --> | ||
These two morphs are used on the [[ | These two morphs are used on the [[Citrate Synthase]] page. | ||
Revision as of 01:44, 15 November 2010
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.
- 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 File: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 File:CA1ctsTO2cts.pdb.gz .
|
These two morphs are used on the Citrate Synthase page.
