User:Wayne Decatur/1cts to 2cts (citrate synthase) morph methods: Difference between revisions
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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 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 | * 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. (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 references to model numbers from these 3 files too) | ||
* 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. | ||
