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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*50-90 = N-terminal and is forestgreen
*50-90 = N-terminal and is forestgreen
*91-298 = Domain 1 and is khaki      gold
*91-298 = Domain 1 and is khaki      gold
*304-480 = Domain 2 and is crimson  REALLY USED 297-480  crimson   firebrick    darkred
*304-480 = Domain 2 and is crimson  REALLY USED 297-480  crimson     firebrick    darkred
*chain e is darkseagreen
*chain e is darkseagreen




'''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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structure TURN;
structure TURN;
select 128-132:a and 1.8;
select 128-132:a and 1.8;
structure TURN;
select 297-299:a and 1.8;
structure TURN;
structure TURN;
select 231-236:a and 1.8;
select 231-236:a and 1.8;
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select 297-304:a and 1.2;
select 297-304:a and 1.2;
structure TURN;
structure TURN;
select 1.2;
cartoon on;
select 297-304:a and 1.3;
structure TURN;
select 1.3;
cartoon on;
select 297-304:a and 1.4;
structure TURN;
select 1.4;
cartoon on;
select 297-299:a;
structure TURN;
select protein;
cartoon on;
Later for showing the N-terminal helix stretched from the RNA binding site to the ATP binding site, I wanted just model 1.1 and 1.8 to show up at the same time so I told it to display all and then set display to just those two:
model all;
display (*/1.1,*/1.8);
model all;
*This was described under frame at the [http://chemapps.stolaf.edu/jmol/docs/?ver=11.8#frame Jmol Interactive script documentation] --  "Same as the animation frame command. See also model. Note that you can show specific pairs or sets of frames or models by using frame all followed by display (*/n,*/m,*/p), where n, m, and p are frame numbers."  HOWEVER, WHILE THIS LOOKED GOOD ON THE SCREEN IN PROTEOPEDIA WHEN I PRESSED SAVED SCENE, IT ONLY KEPT SHOWING ONE MODEL WHEN LOADED FROM A GREEN LINK OR FROM LOAD SCENE TAB, which is odd because same thing seems to work for ribosome but that is only two models and both next to each other and all just on and not a subset. (From a later test, it seems it would have worked with a template, but not clear how to load correct molecule if not already loaded - which could be eliminated as a problem if use a jmol window only for that set of models.) So I will make a file like that of the two. And edited the commands fixing secondary structure to match.
select 67-90:a and 1.1;
structure TURN;
select 78-80:a and 1.1;
structure SHEET;
select 94-98:a and 1.1;
structure HELIX;
select 1.1;
cartoon on;
select 297-304:a and 1.1;
structure TURN;
select 428-436:a and 1.1;
structure TURN;
select 466-470:a and 1.1;
structure TURN;
select 1.1;
cartoon on;
select 72-74:a and 1.2;
structure TURN;
select 94-98:a and 1.2;
structure HELIX;
select 128-132:a and 1.2;
structure TURN;
select 128-132:a and 1.2;
structure TURN;
select 297-299:a and 1.2;
structure TURN;
select 231-236:a and 1.2;
structure HELIX;
select 460-468:a and 1.2;
structure TURN;
select 464-466:a and 1.2;
structure SHEET;
select 1.2;
select 1.2;
cartoon on;
cartoon on;
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-->
-->


<scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Ddx19morph/3'>TextToBeDisplayed</scene>
<scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Ddx19morph/7'>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>
<scene name='User:Wayne_Decatur/3ewsSLASH3g0h_Morph_methods/Openclosedboth/8'>both</scene>
The <scene name='3dmq/Rapa/1'>biological molecule is a single-chain RapA monomer</scene>.<br>
{{Template:Link Test template}}
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"/>
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