First time at Proteopedia? Click on the green links: they change the 3D image. Click and drag the molecules. Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, you can edit pages in Proteopedia. Visit the Main Page to learn more.
User:Wayne Decatur/3fpn Morph methods
Moving to match Figure 3
Using Pymol and the 3fpn file, I moved so interface is perpendicular to y axis:
translate [10,0,0], chain b
rotate y, 65, chain b
Morph from normal 3fpn structure to view in Figure 3 of article describing the structure
Insert caption here
Took the two files and submitted them. Since the structures didn't have nucleic acids, I took the advice here and used the Yale Morph Server for morphing complexes. I got the e-mail and followed the link to a Jmol animation of the morph. I right clicked on the Jmol frank and click the top entry in the menu and then the bottom spot in the menu that came up to download the structures in the morph.
Uploaded to Proteopedia Image:3fpntorotatedversion.pdb.
loaded '3fpntorotatedversion.pdb' in Scene Authoring Tools.
[Control the animation with the 'animation' submenu on the menu that comes up if you click on the Jmol frank in the bottom rigth corner. Also, if the animation seems to be stuck, scroll in the bar on the right of your browser.]
THIS STUFF WAS TESTING OUT USING 'model all;' command in the CONSOLE. IT WASN'T WORKING WITH 3fpntorotatedversion.pdb loaded into Scene authoring tools but it did work right with 3fpntest.pdb WHERE I HAD FIXED THE MODEL NUMBERING AND END MODEL AND END INFO AND THE TITLE SIGNAL IN THE PDB FILE:
SEE User:Wayne Decatur/3ewsSLASH3g0h Morph methods FOR more on this 'model all;' command stuff because problem seems to be that Yale Morph server starts it off with 'Model 0'??!?! Or is in number of models? See bottom of that page.