User talk:Wayne Decatur/Sandbox 1 vs 21 vs 2 vs 12

From Proteopedia

The structure used on this page can be found Image:Rpr2 snm1 1x0t rpa12FIT.pdb, along with a link to a resource describing how it was made.

Most (ALL?) of the code for each scene is in the page because standard approaches wouldn't work with these complex scenes.

Technical roadblocks/ hurdles:

• I've had it take about a dozen times of submitting the same page to get the updated page posted to Proteopedia. Often after submitting I am faced with the message

   Sorry! We could not process your edit due to a loss of session data. Please try again. If it still doesn't work, try logging out and logging back in.

  and I need to hit the `Save page` button over and over again. (Ironically, I was up to nine attempts just to add this note to the `talk` page. Tenth worked!)

• In a script within the wikitext this line worked:

select 1-150:A and model=3; color opaque [x69509b];select 65-109:A and model=3; color opaque mediumpurple; select ZN and model=3; color opaque CPK;

while this one below caused a compiler error when I tried to run the script!?!?! ( I had to open the console before running the script to see this.)

select :A and model=3; color opaque [x69509b];select 65-109:A and model=3; color opaque mediumpurple; select ZN and model=3; color opaque CPK;

It seems rather unstable if not having a number there breaks it when `select :A and model=3; ` works pasted into the console!?!?

• For some reason, the third strand of the beta-sheet in Rpr2p doesn't like to show up. I tried adding it to the scene with the following.

select 120-124:K and model 1; structure SHEET;cartoon on;

However, while it looks to work in the scene authoring tools before I save it, when I load the scene on the page the change is not made!!?!? I thought a similar approach worked before here?

I ended up making 'fake' scene link buttons and ... For now I am saying something to the effect of: "I load all the four structures as grey to start at a basic point in order to subsequently emphasize the structural feature in each by highlighting it using the follow scene link. Click on the green text to open the scene." However, in actuality, a technical constraint that I cannot get the models to open with the applied secondary structure is the reason for going that way.

• I tried adding echos that would go on when I toggled on each structure. Addition of the toggles using the code below broke the toggles. I originally tried without quotes around the text to be in the echos. The code came from my Rpr2p hosted on Pythonannywhere.com and so it should work EXCEPT THAT DIDN'T HAVE MULTIPLE MODELS. That would explain why they wouldn't work perhaps. Ended up giving up idea of having them.

models 0; display add 1.1; display remove 1.2; display remove 1.3; display remove 1.4;
</script>
  <text>Start with just Rpr2p shown to work with controls below</text>.
 </jmolLink>
</jmol>
<br>Controls for the feature in specific chains:<br>
<jmol>
 <jmolCheckbox>
  <scriptWhenChecked>models 0; display add 1.1;set echo rpr2 [3 94%]; set echo rpr2 LEFT;echo "◼ Rpr2p";color echo crimson;</scriptWhenChecked>
  <scriptWhenUnchecked>models 0; display remove 1.1;set echo rpr2 HIDDEN;</scriptWhenUnchecked>
<checked>true</checked>
  <text>Rpr2p on/off</text>
 </jmolCheckbox>
</jmol>
<jmol>
 <jmolCheckbox>
  <scriptWhenChecked>models 0; display add 1.2; display add 1.1 and ZN;set echo snm1 [3 88%]; set echo snm1p LEFT;echo "◼ Snm1p";color echo tomato;</scriptWhenChecked>
  <scriptWhenUnchecked>models 0; display remove 1.2; display remove 1.1 and ZN;set echo snm1 HIDDEN;</scriptWhenUnchecked>
<checked>false</checked>
  <text>Snm1p on/off </text><font color = 'tomato'>Snm1p(theoretical)</font>
 </jmolCheckbox>
</jmol>
<jmol>
 <jmolCheckbox>
  <scriptWhenChecked>models 0; display add 1.3;set echo rpp21 [3 82%]; set echo rpp21 LEFT;echo "◼ Rpp21p";color echo dodgerblue;</scriptWhenChecked>
  <scriptWhenUnchecked>models 0; display remove 1.3;set echo rpp21 HIDDEN;</scriptWhenUnchecked>
  <text>Rpp21p on/off</text>
 </jmolCheckbox>
</jmol>
<jmol>
 <jmolCheckbox>
  <scriptWhenChecked>models 0; display add 1.4;set echo rpa12 [3 76%]; set echo rpa12 LEFT;echo "◼ Rpa12p";color echo mediumpurple;</scriptWhenChecked>
  <scriptWhenUnchecked>models 0; display remove 1.4;set echo rpa12 HIDDEN;</scriptWhenUnchecked>
  <text>Rpa12p (Rrn4p) on/off</text>
 </jmolCheckbox>
</jmol>