User:Eric Martz/Sandbox 3

ConSurf PrototypeConSurf Prototype

spinqualitylabelsall models PDB ID 2hhd Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
2hhd, resolution 2.20Å ()
Ligands:	,
Structural annotation: Resources: CATH : 2Hhda00, 2Hhdb00, 2Hhdc00, 2Hhdd00 InterPro : Ipr002339, Ipr002338, Ipr000971, Ipr009050, Ipr002337, Ipr012292 Pfam : PF00042 SCOP : d2hhda_, d2hhdb_, d2hhdc_, d2hhdd_ UniProt : P69905, P68871
Functional annotation: Cellular component: hemoglobin complex Biological process: transport oxygen transport positive regulation of nitric oxide biosynthetic process nitric oxide transport regulation of blood vessel size regulation of blood pressure Molecular function: oxygen binding protein binding metal ion binding oxygen transporter activity heme binding iron ion binding hemoglobin binding selenium binding
Evolutionary conservation: Toggle Conservation Colors: Rows = identical sequences: Further Information: Caveats, Explanation, Complete Results at ConSurfDB
Resources:	FirstGlance, OCA, RCSB, PDBsum
Coordinates:	save as pdb, mmCIF, xml

ScenesScenes

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)

Button TestsButton Tests

Lower case x so it doesn't look like chain X. Two spaces in empty [ ]. Uses document.getElementById('jmb_A').value='...'. Works in

• Internet Explorer 7/Windows XP
• Internet Explorer 6/Windows 98
• Firefox2/Windows 98/Windows XP
• Firefox2/OSX
• Safari/OSX (mouse movement needed to get the text change, else button label is always one step behind).

Uses bB.value='...'. Firefox: javascript error, bB is not defined, so no button text change in Firefox. Firefox every second click ignored unless mouseout between clicks. Works in Safari/OSX and Internet Explorer 6/7/Windows.

Checkmark: ✓ but if it is used in the button text label, the previous characters don't appear. Could maybe use a button label ✓A instead of A[✓], but haven't tested it. And in Internet Explorer 7, this "checkmark" appears as two horizontal bars. Not worth pursuing, I think. (Similarly, I often see problems with greek letters, so it is better to spell them out in English than to try to show the actual greek letter.)

User Interface & Color KeyUser 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.
• When a chain is "checked" [x], it will be colored 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:

Evolutionary Conservation:                     [show]

After expanding, it could look like this (using buttons):

Evolutionary Conservation:                       [hide]
Toggle Conservation Colors:	Rows = identical sequences:
Further Information:	Explanation Complete results at ConSurf

ScriptsScripts

When the Evolutionary Conservation block is expanded, a master script is run that colors and spacefills all chains.

The scripts below are designed to work both for single-model X-ray files, and for NMR Ensembles of Models. In the latter, the scripts show only model 1 for ConSurf scenes (frame 1.1).

Changing a CheckboxChanging a Checkbox

After a chain checkbox (in the expanded Evolutionary Conservation block) 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.

Design Goals for ConSurf ScriptsDesign Goals for ConSurf Scripts

ConSurfDB generates one script per chain. Proteopedia will generate, from these, a single consolidated script for each PDB entry. The initial view, shown automatically when the Evolutionary Conservation block is expanded, will be produced by the consolidated script, and will apply ConSurf colors to all chains concurrently. An example is the ConSurf color all 4 chains green linked scene above. The ConSurf team does not show such an all-chain view for hetero-oligomers because the conservation level colors are relative, and do not have the same quantitative conservation level meanings in sequence-different chains. Proteopedia will explain this, but will provide an all-chain view as the initial view. Individual chains can then be de-colored with the checkboxes.

In order to have to generate just a single ConSurf script per PDB file, that single consolidated script must serve two purposes. It must generate the desired initial view when the Evolutionary Conservation block is expanded, and it must serve the SAT Colors dialog, enabling the user to apply ConSurf colors to any selected protein moiety.

Note that (possibly) in contrast to the scripts at ConSurfDB, 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. Once these are defined, the scripts avoid re-defining them when called again, to save execution time.

Top Level ConSurf ScriptTop Level ConSurf Script

This is the script sent to Jmol when the Evolutionary Conservation block is expanded.

select protein
define ~consurf_to_do selected
consurf_spacefill = true
script "wiki/ConSurf/hh/2hhd_consurf.spt"

---

script "/wiki/scripts/allRenderingsOff.spt"

select hetero and not water spacefill 0.5 wireframe 0.3 color cpk dots

if (!consurf_levels_defined) script "/wiki/ConSurf/hh/2hhd_consurf.spt" endif select protein define ~consurf_to_color selected script consurf_color_levels.spt

select protein spacefill backbone 0.4 color backbone [xc8c8c8]

select nucleic cartoon color cpk

consurf_color_levels.sptconsurf_color_levels.spt

The purpose of this script is to color all, or any subset, of protein atoms according to ConSurf. This script is "constant": the same for all PDB entries. A big advantage of this script is that it sets the ConSurf color RGB values. If any ever need to be changed, only this one script needs changing. This script requires that the atom subset term ~consurf_to_color be defined beforehand. It also requires that 2hhd_consurf.spt has been run beforehand.

# Any protein atoms not assigned a consurf level, e.g. short peptides not processed by consurf,
# will remain the following color.
select ~consurf_to_color
color yellow

# Each consurf level is now colored with the standard consurf colors.
select ~consurf_to_color and ~con10
color [255,255,150]
select ~consurf_to_color and ~con9
color [160,37,96]
select ~consurf_to_color and ~con8
color [240,125,171]
select ~consurf_to_color and ~con7
color [250,201,222]
select ~consurf_to_color and ~con6
color [252,237,244]
select ~consurf_to_color and ~con5
color [255,255,255]]
select ~consurf_to_color and ~con4
color [234,255,255]
select ~consurf_to_color and ~con3
color [215,255,255]
select ~consurf_to_color and ~con2
color [140,255,255]
select ~consurf_to_color and ~con1
color [16,200,209]

2hhd_consurf.spt2hhd_consurf.spt

1. This script defines ~con1, ~con2, ... ~con10, the atoms in each consurf level, unless they have already been defined in a previous execution of this script (see consurf_levels_defined). The amino acids per color grade are combined into each ~con## term for all chains as shown in the example script below.
2. This script applies ConSurf colors to the protein atoms included in ~consurf_to_color (which must therefore be defined before calling this script).
3. This script spacefills the atoms it colors only if consurf_spacefill is true. Therefore, consurf_spacefill must be set before calling this script.
4. Wherever possible, this script calls other scripts to separate commands that are not PDB-ID specific, so they can be maintained separately.

# generated from ConSurf files dated 2008-06-12
script "/wiki/scripts/allRenderingsOff.spt";
select hetero and not water
spacefill 0.5
wireframe 0.3
color cpk
dots

define ~con10 none
select PHE71, PHE85, PHE118
select selected and :B
select selected or ~con10
define ~con10 selected
select PHE71, PHE85, PHE118
select selected and :D
select selected or ~con10
define ~con10 selected
color [255,255,150]

define ~con9 none
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
select selected or ~con9
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
select selected or ~con9
define ~con9 selected
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 :C
select selected or ~con9
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 :D
select selected or ~con9
define ~con9 selected
color [160,37,96]

define ~con8 none
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
select selected or ~con8
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
select selected or ~con8
define ~con8 selected
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 :C
select selected or ~con8
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 :D
select selected or ~con8
define ~con8 selected
color [240,125,171]

define ~con7 none
select MET32, LEU66, ASP75, ALA79, LEU80, HIS103, VAL107, THR108, ALA110, PHE117
select selected or THR137, SER138
select selected and :A
select selected or ~con7
define ~con7 selected
select VAL11, LYS17, GLU26, ALA27, GLY29, LEU31, THR84, LYS95, GLN131, VAL134
select selected and :B
select selected or ~con7
define ~con7 selected
select MET32, LEU66, ASP75, ALA79, LEU80, HIS103, VAL107, THR108, ALA110, PHE117
select selected or THR137, SER138
select selected and :C
select selected or ~con7
define ~con7 selected
select VAL11, LYS17, GLU26, ALA27, GLY29, LEU31, THR84, LYS95, GLN131, VAL134
select selected and :D
select selected or ~con7
define ~con7 selected
color [250,201,222]

define ~con6 none
select TRP14, ALA28, PRO44, LYS60, HIS72, SER81, LYS90, SER102, CYS104, SER133
select selected and :A
select selected or ~con6
define ~con6 selected
select HIS2, LEU3, VAL33, ALA70, GLY74, HIS77, ALA86, VAL113, LEU114, THR123
select selected or PRO124, LYS144
select selected and :B
select selected or ~con6
define ~con6 selected
select TRP14, ALA28, PRO44, LYS60, HIS72, SER81, LYS90, SER102, CYS104, SER133
select selected and :C
select selected or ~con6
define ~con6 selected
select HIS2, LEU3, VAL33, ALA70, GLY74, HIS77, ALA86, VAL113, LEU114, THR123
select selected or PRO124, LYS144
select selected and :D
select selected or ~con6
define ~con6 selected
color [252,237,244]

define ~con5 none
select VAL17, ALA26, PHE36, LYS56, VAL70, LEU100, LEU106, VAL121
select selected and :A
select selected or ~con5
define ~con5 selected
select THR4, ASN19, LYS65, ASN80, VAL111, ALA128, VAL133, GLY136, HIS143
select selected and :B
select selected or ~con5
define ~con5 selected
select VAL17, ALA26, PHE36, LYS56, VAL70, LEU100, LEU106, VAL121
select selected and :C
select selected or ~con5
define ~con5 selected
select THR4, ASN19, LYS65, ASN80, VAL111, ALA128, VAL133, GLY136, HIS143
select selected and :D
select selected or ~con5
define ~con5 selected
color [255,255,255]

define ~con4 none
select HIS20, ALA21, LEU48, SER49, MET76, PRO77, LEU109, ALA120
select selected and :A
select selected or ~con4
define ~con4 selected
select GLU6, THR50, VAL54, LYS59, LEU68, SER72, HIS117
select selected and :B
select selected or ~con4
define ~con4 selected
select HIS20, ALA21, LEU48, SER49, MET76, PRO77, LEU109, ALA120
select selected and :C
select selected or ~con4
define ~con4 selected
select GLU6, THR50, VAL54, LYS59, LEU68, SER72, HIS117
select selected and :D
select selected or ~con4
define ~con4 selected
color [234,255,255]

define ~con3 none
select ASN9, VAL10, LYS11, SER35, THR38, HIS50, VAL55, HIS89, LEU125, ALA130
select selected or THR134
select selected and :A
select selected or ~con3
define ~con3 selected
select VAL20, MET55, LYS61, VAL109, ALA142
select selected and :B
select selected or ~con3
define ~con3 selected
select ASN9, VAL10, LYS11, SER35, THR38, HIS50, VAL55, HIS89, LEU125, ALA130
select selected or THR134
select selected and :C
select selected or ~con3
define ~con3 selected
select VAL20, MET55, LYS61, VAL109, ALA142
select selected and :D
select selected or ~con3
define ~con3 selected
color [215,255,255]

define ~con2 none
select GLU30, ALA53, THR67, ALA71, ALA82, LEU105, PRO114, LEU129
select selected and :A
select selected or ~con2
define ~con2 selected
select GLY25, LEU75, ALA76, LYS120, GLU121
select selected and :B
select selected or ~con2
define ~con2 selected
select GLU30, ALA53, THR67, ALA71, ALA82, LEU105, PRO114, LEU129
select selected and :C
select selected or ~con2
define ~con2 selected
select GLY25, LEU75, ALA76, LYS120, GLU121
select selected and :D
select selected or ~con2
define ~con2 selected
color [140,255,255]

define ~con1 none
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
select selected or ~con1
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
select selected or ~con1
define ~con1 selected
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 :C
select selected or ~con1
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 :D
select selected or ~con1
define ~con1 selected
color [16,200,209]

consurf_levels_defined = true
select protein
spacefill
backbone 0.4
color backbone [xc8c8c8]
select nucleic
cartoon
color cpk