User:Eric Martz/Sandbox 3
From Proteopedia
| Line 20: | Line 20: | ||
<jmol> | <jmol> | ||
<jmolButton> | <jmolButton> | ||
| - | <script>if (~A) | + | <script>if (~A); select:A; spacefill off; ~A = 0;javascript "bA.value='A off'"; else; select:A; spacefill on; ~A = 1;javascript "bA.value='A on'"; endif;</script> |
<text>A on</text> | <text>A on</text> | ||
<name>bA</name> | <name>bA</name> | ||
Revision as of 13:27, 4 July 2008
Contents |
ConSurf Prototype
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| 2hhd, resolution 2.20Å () | |||||||||
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| Ligands: | , | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Scenes
Opening the proposed Evolutionary Conservation section below the molecule would automatically color all chains by ConSurf, and spacefill them. Checkboxes in this section, one per chain, would be checked when the section is first opened. Unchecking a given chain would render it as a gray backbone (as in ConSurf). Ligands will be ball and stick, with dot surfaces, colored by element (as in ConSurf; oops, forgot to do the sulfates in some scenes). Here, for demonstration purposes, are 5 of the 16 possible scenes that 4-chain-checkboxes could generate:
- (2 alphas, A and C, and 2 betas, B and D, in 2HHD).
- (one alpha, one beta)
- (both alphas)
User Interface & Color Key
To keep the user interface simple in Proteopedia, at least to start with, I propose that the only controls will be one checkbox per chain to ConSurf-color+spacefill each chain or not. The color key will not be interactive (unlike in ConSurf). Clicking the link Complete results at ConSurf will provide a path to the display in FirstGlance in Jmol with many more options.
Below are non-interactive mockups just to suggest the look for a user interface that would be an additional expandable block beneath the molecule.
- Links do not work.
- [✓] represents a checkbox. When checked, it will color the chain by conservation, and spacefill it. When unchecked, that chain will become a gray backbone trace.
- The link to Explanation would go to a Proteopedia page of explanation. It might be a revised version of Conservation, Evolutionary.
Before expanding this section, it could look like this:
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Evolutionary Conservation: [show] |
After expanding, it could look like this:
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Evolutionary Conservation: [hide] | |
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Hide all conservation colors. | |
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Click Chain(s) to Show Conservation: | Rows = identical sequences: A C |
| Further Information: |
Explanation
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Scripts
When the Evolutionary Conservation block is expanded, a master script is run that colors and spacefills all chains.
The scripts below will need to be tweaked a bit for NMR Ensembles of Models. In these, we will want to show only model 1 for ConSurf scenes.
Changing a Checkbox
After a checkbox is changed, the currently checked chains are put into this script:
select protein spacefill off select (:a,:c) # LIST OF CHECKED CHAINS spacefill
The gray backbones for all chains are always rendered, but are hidden within spacefilled atoms, when a chain is spacefilled. Once set, the colors never change. Although the backbones are gray, the atoms are ConSurf-colored. All a checkbox needs to do is spacefill the appropriate set of chains. The colors remain.
Master ConSurf Script
The master script will need to be generated by ConSurf for each PDB code. It differs in a few minor ways from the per-chain scripts currently being generated.
- All chains are colored and spacefilled, not just one chain. This includes both sequence-identical chains, and sequence different chains.
- The 10 color grade groups of residues are selected only once, for all chains, as shown in the example script below.
- The defined Jmol variables ~con1, ~con2, ... ~con10 now each begin with a tilde (~). This is the recommended practice for such variables in Jmol, to avoid possible conflicts.
MASTER SCRIPT
# insert allRenderingsOff script (already in use for NMR) select hetero and not water spacefill 0.5 wireframe 0.3 color cpk dots script 2hhd_consurf.spt # from pre-calculated ConSurf dataset, one per PDB code select protein backbone 0.4 color backbone [xc8c8c8] select nucleic cartoon color cpk
2hhd_consurf.spt
In the example of 2hhd, there are two sets of sequence-identical chains (AC, BD). Each set has a block of amino acid selections for each color grade. The amino acids per color grade are combined for all chains (including sequence-different chains) as shown in the example script below. This script was run to produce the scene above Consurf color all chains.
select none select selected and (:A,:C) define ~con10 selected select PHE71, PHE85, PHE118 select selected and (:B,:D) select selected or ~con10 define con10 selected color [255,255,150] spacefill select LYS7, LYS16, GLU27, ARG31, PHE33, PRO37, THR39, LYS40, THR41, PHE43 select selected or SER52, HIS58, GLY59, LYS61, VAL62, ALA65, ALA69, LEU83, SER84 select selected or HIS87, ALA88, LEU91, ARG92, VAL93, ASP94, PRO95, ASN97, PHE98 select selected or LEU101, HIS122, SER124, ASP126, LYS127, VAL132, LEU136 select selected or LYS139, TYR140, ARG141 select selected and (:A,:C) define ~con9 selected select VAL1, GLU7, LYS8, TRP15, GLY24, ARG30, LEU32, VAL34, TYR35, PRO36, TRP37 select selected or THR38, ARG40, PHE42, PHE45, GLY46, SER49, ALA53, ASN57, VAL60 select selected or ALA62, HIS63, GLY64, LYS66, VAL67, ASP79, LEU81, LYS82, LEU88 select selected or SER89, GLU90, HIS92, LEU96, VAL98, PRO100, ASN102, PHE103 select selected or LEU106, PHE122, GLN127, LYS132, VAL137, ALA140, TYR145 select selected or HIS146 select selected and (:B,:D) select selected or ~con9 define ~con9 selected color [160,37,96] spacefill select VAL1, LEU2, SER3, ASP6, GLY25, LEU29, TYR42, HIS45, PHE46, ASP47, GLY51 select selected or GLN54, ASP74, ASP85, LEU86, VAL96, LYS99, HIS112, THR118 select selected or PRO119, ALA123, PHE128, VAL135 select selected and (:A,:C) define ~con8 selected select VAL18, LEU28, GLN39, PHE41, ASP47, LEU48, LEU91, CYS93, ASP94, HIS97 select selected or ASP99, GLU101, LEU105, GLY107, ASN108, ALA115, ALA129, ALA138 select selected or LEU141 select selected and (:B,:D) select selected or ~con8 define ~con8 selected color [240,125,171] spacefill select MET32, LEU66, ASP75, ALA79, LEU80, HIS103, VAL107, THR108, ALA110, PHE117 select selected or THR137, SER138 select selected and (:A,:C) define ~con7 selected select VAL11, LYS17, GLU26, ALA27, GLY29, LEU31, THR84, LYS95, GLN131, VAL134 select selected and (:B,:D) select selected or ~con7 define ~con7 selected color [250,201,222] spacefill select TRP14, ALA28, PRO44, LYS60, HIS72, SER81, LYS90, SER102, CYS104, SER133 select selected and (:A,:C) define ~con6 selected select HIS2, LEU3, VAL33, ALA70, GLY74, HIS77, ALA86, VAL113, LEU114, THR123 select selected or PRO124, LYS144 select selected and (:B,:D) select selected or ~con6 define ~con6 selected color [252,237,244] spacefill select VAL17, ALA26, PHE36, LYS56, VAL70, LEU100, LEU106, VAL121 select selected and (:A,:C) define ~con5 selected select THR4, ASN19, LYS65, ASN80, VAL111, ALA128, VAL133, GLY136, HIS143 select selected and (:B,:D) select selected or ~con5 define ~con5 selected color [255,255,255] spacefill select HIS20, ALA21, LEU48, SER49, MET76, PRO77, LEU109, ALA120 select selected and (:A,:C) define ~con4 selected select GLU6, THR50, VAL54, LYS59, LEU68, SER72, HIS117 select selected and (:B,:D) select selected or ~con4 define ~con4 selected color [234,255,255] spacefill select ASN9, VAL10, LYS11, SER35, THR38, HIS50, VAL55, HIS89, LEU125, ALA130 select selected or THR134 select selected and (:A,:C) define ~con3 selected select VAL20, MET55, LYS61, VAL109, ALA142 select selected and (:B,:D) select selected or ~con3 define ~con3 selected color [215,255,255] spacefill select GLU30, ALA53, THR67, ALA71, ALA82, LEU105, PRO114, LEU129 select selected and (:A,:C) define ~con2 selected select GLY25, LEU75, ALA76, LYS120, GLU121 select selected and (:B,:D) select selected or ~con2 define ~con2 selected color [140,255,255] spacefill select PRO4, ALA5, THR8, ALA12, ALA13, GLY15, GLY18, ALA19, GLY22, GLU23, TYR24 select selected or LEU34, GLY57, ALA63, ASP64, ASN68, VAL73, ASN78, ALA111 select selected or LEU113, ALA115, GLU116, SER131 select selected and (:A,:C) define ~con1 selected select PRO5, SER9, ALA10, THR12, ALA13, LEU14, GLY16, ASP21, GLU22, VAL23, GLU43 select selected or SER44, PRO51, ASP52, GLY56, PRO58, GLY69, ASP73, LEU78, GLY83 select selected or THR87, ARG104, LEU110, CYS112, HIS116, GLY119, PRO125, VAL126 select selected or TYR130, ALA135, ASN139 select selected and (:B,:D) select selected or ~con1 define ~con1 selected color [16,200,209] spacefill
