Proteopedia talk:Development: Difference between revisions
Focus on ligands and sites - proposals for improvement |
Focus on ligands and sites - proposals for improvement |
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Focus on ligands and sites when their green links are clicked. | Focus on ligands and sites when their green links are clicked. | ||
* '''Current state:''' the selected entity becomes the center of rotation, and the molecule is zoomed onto it (80% of the JSmol panel). Residues within 4 Â are highlighted with sidechains | * '''Current state:''' the selected entity becomes the center of rotation, and the molecule is zoomed onto it (80% of the JSmol panel). Residues within 4 Â are highlighted with sticks for sidechains and labels for beta carbons. (The script is applied by pdbligand.php) | ||
<pre>define ligContact within(4.0, [HEM]) and protein; | <pre>define ligContact within(4.0, [HEM]) and protein; | ||
define ligContact within(group,ligContact); | define ligContact within(group,ligContact); | ||
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select all; | select all; | ||
</pre> | </pre> | ||
* Proposal A: select only the first ligand of the set, by looking for first chain and first residue in it. Then, label and focus on that one as before. | * '''Problem:''' when there are several ligands of the same name, the focus acts on their geometric center, with a not too helpful result. Example: 4 heme groups in hemoglobin, center is on the whole model. It would be better to focus on just the first heme group. | ||
* '''Proposal A:''' select only the first ligand of the set, by looking for first chain and first residue in it. Then, label and focus on that one as before. | |||
<pre>nc = {[HEM]}.chainNo.min; | <pre>nc = {[HEM]}.chainNo.min; | ||
define ligOne [HEM] and chainNo=nc; | define ligOne [HEM] and chainNo=nc; | ||
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</pre> | </pre> | ||
* Proposal B: label all but zoom in on the first one. | * '''Proposal B:''' label all but zoom in on the first one. | ||
<pre>define ligContact within(4.0, [HEM]) and protein; | <pre>define ligContact within(4.0, [HEM]) and protein; | ||
define ligContact within(group,ligContact); | define ligContact within(group,ligContact); | ||
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zoomTo 0.5 {selected} 0 *0.8; | zoomTo 0.5 {selected} 0 *0.8; | ||
select all; | select all; | ||
</pre> | </pre> | ||
* Proposal C: additionally, if the ligand is very small (e.g. Zn2+), zoom should be reduced, maybe checking its size or mass within the Jmol script. | * '''Proposal C:''' additionally, if the ligand is very small (e.g. Zn2+), zoom should be reduced, maybe checking its size or mass within the Jmol script. | ||