User:Wayne Decatur/3ewsSLASH3g0h Morph methods
From Proteopedia
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<applet load='3g0h' size='300' frame='true' align='right' caption='Insert caption here' /> | <applet load='3g0h' size='300' frame='true' align='right' caption='Insert caption here' /> | ||
Took the two files and submitted them. | Took the two files and submitted them. | ||
| - | + | The structures did have nucleic acids; however, in the past I knew [http://molmovdb.org/cgi-bin/beta.cgi the beta server] handled them so I used it. (This time the result just had chain A since I didn't have the nucleic in both structures.) | |
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| + | 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. | ||
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| + | By the way, the structure that came back from the server didn't have secondary structure when I looked at it in PyMol so I chose from the action meni on the right 'assign sec. str.' and it assigned it (for viewing) for all models and was very close to the crystal secondary structure. Since I didn't save this though, it didn't affect the Morph file. | ||
Uploaded to Proteopedia [[Image:3fpntorotatedversion.pdb]]. <br> | Uploaded to Proteopedia [[Image:3fpntorotatedversion.pdb]]. <br> | ||
Revision as of 04:03, 31 October 2009
Morph from 3ews to 3g0h structure
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Took the two files and submitted them. The structures did have nucleic acids; however, in the past I knew the beta server handled them so I used it. (This time the result just had chain A since I didn't have the nucleic in both structures.)
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.
By the way, the structure that came back from the server didn't have secondary structure when I looked at it in PyMol so I chose from the action meni on the right 'assign sec. str.' and it assigned it (for viewing) for all models and was very close to the crystal secondary structure. Since I didn't save this though, it didn't affect the Morph file.
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 right corner. Also, if the animation seems to be stuck, scroll in the bar on the right of your browser.]
Paper on the structure
- Collins R, Karlberg T, Lehtio L, Schutz P, van den Berg S, Dahlgren LG, Hammarstrom M, Weigelt J, Schuler H. The DEXD/H-box RNA helicase DDX19 is regulated by an {alpha}-helical switch. J Biol Chem. 2009 Apr 17;284(16):10296-300. Epub 2009 Feb 25. PMID:19244245 doi:10.1074/jbc.C900018200
