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(Difference between revisions)
(Focus on ligands and sites - proposals for improvement) |
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</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. | ||
| + | |||
* 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. | * 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= | + | define ligOne [HEM] and chainNo=nc; |
nc = {ligOne}.resNo.min; | nc = {ligOne}.resNo.min; | ||
define ligOne ligOne and resNo=nc; | define ligOne ligOne and resNo=nc; | ||
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zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8; | zoomTo 0.5 { (ligOne , ligContact )} 0 *0.8; | ||
</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; | ||
| Line 35: | Line 37: | ||
nc = {[HEM]}.chainNo.min; | nc = {[HEM]}.chainNo.min; | ||
| - | define ligOne [HEM] and chainNo= | + | define ligOne [HEM] and chainNo=nc; |
nc = {ligOne}.resNo.min; | nc = {ligOne}.resNo.min; | ||
define ligOne ligOne and resNo=nc; | define ligOne ligOne and resNo=nc; | ||
Revision as of 15:16, 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;
- 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;
- 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;
- 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.
