User:Wayne Decatur/3ewsSLASH3g0h Morph methods: Difference between revisions
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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 menu on the right 'assign sec. str.' and it assigned it for all models and was very close to the crystal secondary structure. Since it seemed to be just for viewing and I didn't save this though, it didn't affect the morph file. | 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 menu on the right 'assign sec. str.' and it assigned it for all models and was very close to the crystal secondary structure. Since it seemed to be just for viewing and I didn't save this though, it didn't affect the morph file. | ||
Since the morph file that came back just had the protein from chain A from each endpoint structure, I added back the other parts from 3ews to model 1 and the other parts of 3g0h to Model 8. | Since the morph file that came back just had the protein from chain A from each endpoint structure, I added back the other parts (ligands and RNS, etc.) from 3ews to model 1 and the other parts of 3g0h to Model 8. | ||
However, while that worked for model 8, the ligand of model 1 was off to the side because it needed translating to where model 1 was in the morph which is not the same as 3ews. To move, I copied the 3ews part from the morph and opened it in Swiss-PDB Viewer. Then with MagicFit allowed in 'Loading protein' under preference, I loaded the actual 3ews pdb file. Then I saved the new layer and extracted the information for ADP and placed that as the ADP heteratom information in the Morph file for model 1. | However, while that worked for model 8, the ligand of model 1 was off to the side because it needed translating to where model 1 was in the morph which is not the same as 3ews. To move, I copied the 3ews part from the morph and opened it in Swiss-PDB Viewer. Then with MagicFit allowed in 'Loading protein' under preference, I loaded the actual 3ews pdb file. Then I saved the new layer and extracted the information for ADP and placed that as the ADP heteratom information in the Morph file for model 1. After doing that, I realized the first few residues of 3ews were missing too because they were absent in 3g0h and so I extracted the information fro them as well from the file and added them to the model 1 of the morph. | ||
Uploaded to Proteopedia [[Image: | Uploaded to Proteopedia [[Image:3ews3g0hmorphBETTER.pdb.gz]]. <br> | ||
loaded ' | loaded '3ews3g0hmorphBETTER.pdb.gz' in Scene Authoring Tools.<br> | ||
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* | *50-90 = N-terminal and is forestgreen | ||
*91-298 = Domain 1 and is gold | *91-298 = Domain 1 and is khaki gold | ||
*304-480 = Domain 2 and is darkred | *304-480 = Domain 2 and is crimson REALLY USED 297-480 firebrick darkred | ||
*chain e is darkseagreen | *chain e is darkseagreen | ||
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select 78-80:a and 1.1; | select 78-80:a and 1.1; | ||
structure SHEET; | structure SHEET; | ||
select 94-98:a and 1.1; | |||
structure HELIX; | |||
select 1.1; | select 1.1; | ||
cartoon on; | cartoon on; | ||
| Line 39: | Line 41: | ||
select 1.1; | select 1.1; | ||
cartoon on; | cartoon on; | ||
select 72-74:a and 1.8; | |||
structure TURN; | |||
select 94-98:a and 1.8; | |||
structure HELIX; | |||
select 128-132:a and 1.8; | |||
structure TURN; | |||
select 128-132:a and 1.8; | |||
structure TURN; | |||
select 231-236:a and 1.8; | |||
structure HELIX; | |||
select 1.8; | |||
cartoon on; | |||
<!-- | <!-- | ||
| Line 44: | Line 59: | ||
--> | --> | ||
<scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/ | <scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Ddx19morph/1'>TextToBeDisplayed</scene> | ||
<nowiki>[</nowiki>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.<nowiki>]</nowiki> | <nowiki>[</nowiki>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.<nowiki>]</nowiki> | ||
==Paper on the structure== | ==Paper on the structure== | ||
<ref group="xtra">PMID:19244245</ref><references group="xtra"/> | <ref group="xtra">PMID:19244245</ref><references group="xtra"/> | ||
