User:Wayne Decatur/3ewsSLASH3g0h Morph methods: Difference between revisions
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==Morph from 3ews to 3g0h structure== | ==Morph from 3ews to 3g0h structure== | ||
<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' /> | ||
<scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Ddx19morphback/1'>Pre-hydrolysis (RNA and ATP bound) to post-hydrolysis (ADP bound)</scene>.<br> | |||
Took the two files and submitted them. (Did it with 8 total models.) | Took the two files and submitted them. (Did it with 8 total models.) | ||
The structures did have nucleic acids; however, I knew from past experience [http://molmovdb.org/cgi-bin/beta.cgi the beta server] handled them (even though it sitll says it will be updated to handle it) so I used it. (This time though the result just had chain A since I didn't have the nucleic in both structures.) | The structures did have nucleic acids; however, I knew from past experience [http://molmovdb.org/cgi-bin/beta.cgi the beta server] handled them (even though it sitll says it will be updated to handle it) so I used it. (This time though the result just had chain A since I didn't have the nucleic in both structures.) | ||
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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 RNA, etc.) 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 RNA, 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 | 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:3ews3g0hmorphBETTER.pdb.gz]]. <br> | Uploaded to Proteopedia [[Image:3ews3g0hmorphBETTER.pdb.gz]]. <br> | ||
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'''I'd have to check but I think where I am using <code>structure TURN;</code> below, I probably wanted <code>structure NONE;</code>. The representation is the same except for color and so it worked for the purposes in which I used it here. But it wasn't probably the best way to do it.''' See [[Secondary structure]] and [http://wiki.jmol.org/index.php/Protein_Community here] and [http://chemapps.stolaf.edu/jmol/docs/?search=structure#structure here] and [http://chemapps.stolaf.edu/jmol/docs/?search=structure#setstructure here] for more information. | |||
When the animation played in Jmol the models corresponding to 3ews and 3g0h had regions that should be turns that were showing as helices and beta sheets and so I used structure command to fix. | When the animation played in Jmol the models corresponding to 3ews and 3g0h had regions that should be turns that were showing as helices and beta sheets and so I used structure command to fix. | ||
select 67-90:a and 1.1; | select 67-90:a and 1.1; | ||
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{{Template:Link Test template}} | {{Template:Link Test template}} | ||
<scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Testmodelall/1'>Test using console to enter model all command with the pdb file used in the morph</scene> 3ews3g0hmorphBETTER.pdb.gz | AS I SAW WITH 3fpn's file today: ENTERING 'model all;' INTO THE CONSOLE DOESNT WORK ON THESE FILES FROM YALE SERVER?!?! I assume it is the sever and not the number of models in the file because the 'model all' approach works with the ribosome files I made as well as LepA's files. | ||
<scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Testmodelall/1'>Test using console to enter model all command with the pdb file used in the morph</scene> uses ---->3ews3g0hmorphBETTER.pdb.gz at [[Image:3ews3g0hmorphBETTER.pdb.gz]]. THE SCENE FAILS TO SHOW MORE THAN ONE MODEL!!! | |||
Maybe it is the 'model 0' that Yale Moprh server puts because I was able to use 3ews3g0hJUSTSTARTEND.pdb which I simpled cut out in between models from first and last and made first model 1. Otherwise the formatting is like Yale Morph Server outputs. | |||
<scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'>Testing where first model is 1 and not 0 like Yale Morph server puts</scene> uses ---->3ews3g0hJUSTSTARTEND.pdb.gz at [[Image:3ews3g0hJUSTSTARTEND.pdb.gz]]. | |||
YES IT MUST BE 'model 0' stuff or number of models because <scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/10'>THIS SCENE</scene> WORKS!!!! | |||
==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"/> | ||
