Jmol/Visualizing membrane position: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) No edit summary |
Eric Martz (talk | contribs) No edit summary |
||
| Line 33: | Line 33: | ||
<pre>draw cyl1 cylinder diameter 100.0 color gray (thr607) (leu250)</pre> | <pre>draw cyl1 cylinder diameter 100.0 color gray (thr607) (leu250)</pre> | ||
Adapt this command to your situation, copy and paste it into the LOWER box of the Console, and click the ''Run'' button at the lower-left of the console box. | Adapt this command to your situation, copy and paste it into the LOWER box of the Console, and click the ''Run'' button at the lower-left of the console box. | ||
*''cyl1'' is an arbitrary name for this cylinder. | *''cyl1'' is an arbitrary name for this cylinder. | ||
*You may adjust the diameter and color to your taste. (Gray is a [[DRuMS|standard color]] for hydrophobic. Yellow is sometimes used with the mnemonic ''butter'' in mind.) | *You may adjust the diameter and color to your taste. (Gray is a [[DRuMS|standard color]] for hydrophobic. Yellow is sometimes used with the mnemonic ''butter'' in mind.) | ||
*If you wish to delete all cylinders before making a new one, the command is | *If you wish to delete all cylinders before making a new one, the command is | ||
<pre>draw * delete</pre> | <pre>draw * delete</pre> | ||
*To make the cylinder translucent, the command is | |||
<pre>draw cyl1 color translucent -1</pre> | |||
Once you have the desired cylinder in the SAT, save the scene, insert a green link in the wikitext box, and save the page. Then test the green link. | |||
After displaying the cylinder with your new green link, if you then click a different green link, the cylinder may persist, unwanted. To fix this: | |||
# In the SAT, load the other scene. | |||
**It doesn't matter if the cylinder is not visible in the SAT. | |||
# Open the command console. | |||
# Enter the above ''delete'' command. | |||
# Save the scene. | |||
# Update the green link to use the newly saved version of the scene. | |||
# Test. | |||
