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Proteopedia talk:Development
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(Difference between revisions)
(typo) |
(Focus on ligands and sites - proposals for improvement) |
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| Line 10: | Line 10: | ||
background label yellow; color labels black; | background label yellow; color labels black; | ||
zoomTo 0.5 { ([HEM] , ligContact )} 0 *0.8; | zoomTo 0.5 { ([HEM] , ligContact )} 0 *0.8; | ||
| + | select all; | ||
</pre> | </pre> | ||
* '''Problem:''' when there are several ligands of the same name, the focus act on their center, which is not too helpful. Example: 4 heme groups in hemoglobin. It would be better to focus on just the first one. | * '''Problem:''' when there are several ligands of the same name, the focus act on their center, which is not too helpful. Example: 4 heme groups in hemoglobin. It would be better to focus on just the first one. | ||
| Line 26: | Line 27: | ||
background label yellow; color labels black; | background label yellow; color labels black; | ||
zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8; | zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8; | ||
| + | select all; | ||
</pre> | </pre> | ||
| Line 44: | Line 46: | ||
define ligContact within(group,ligContact); | define ligContact within(group,ligContact); | ||
zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8; | zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8; | ||
| + | select all; | ||
| + | </pre> | ||
| + | or, maybe this end gives a better orientation for focus: | ||
| + | <pre>select (ligOne , ligContact); | ||
| + | rotate best -0.3; | ||
| + | zoomTo 0.5 {selected} 0 *0.8; | ||
| + | select all; | ||
| + | </pre> | ||
</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. | ||
Revision as of 15:36, 25 June 2017
Focus on ligands and sites
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 in sticks and C_beta labeled.
define ligContact within(4.0, [HEM]) and protein;
define ligContact within(group,ligContact);
select ligContact and sidechain; color cpk;
select ligContact and (sidechain,alpha); wireframe 0.3;
select ligContact and *.CB; label %m%r;
background label yellow; color labels black;
zoomTo 0.5 { ([HEM] , ligContact )} 0 *0.8;
select all;
- Problem: when there are several ligands of the same name, the focus act on their center, which is not too helpful. Example: 4 heme groups in hemoglobin. It would be better to focus on just the first one.
- 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.
nc = {[HEM]}.chainNo.min;
define ligOne [HEM] and chainNo=nc;
nc = {ligOne}.resNo.min;
define ligOne ligOne and resNo=nc;
define ligContact within(4.0, ligOne) and protein;
define ligContact within(group,ligContact);
select ligContact and sidechain; color cpk;
select ligContact and (sidechain,alpha); wireframe 0.3;
select ligContact and *.CB; label %m%r;
background label yellow; color labels black;
zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8;
select all;
- Proposal B: label all but zoom in on the first one.
define ligContact within(4.0, [HEM]) and protein;
define ligContact within(group,ligContact);
select ligContact and sidechain; color cpk;
select ligContact and (sidechain,alpha); wireframe 0.3;
select ligContact and *.CB; label %m%r;
background label yellow; color labels black;
nc = {[HEM]}.chainNo.min;
define ligOne [HEM] and chainNo=nc;
nc = {ligOne}.resNo.min;
define ligOne ligOne and resNo=nc;
define ligContact within(4.0, ligOne) and protein;
define ligContact within(group,ligContact);
zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8;
select all;
or, maybe this end gives a better orientation for focus:
select (ligOne , ligContact);
rotate best -0.3;
zoomTo 0.5 {selected} 0 *0.8;
select all;
</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.
