Jmol/Visualizing membrane position: Difference between revisions
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To generate the cylinder in the [[SAT]], click on the button below JSmol ''Advanced: Open JSmol Console''. The command to generate the cylinder will have this form: | To generate the cylinder in the [[SAT]], click on the button below JSmol ''Advanced: Open JSmol Console''. The command to generate the cylinder will have this form: | ||
<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. | |||
*''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.) | |||
*If you wish to delete all cylinders before making a new one, the command is | |||
<pre>draw * delete</pre> | |||
