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_initial_scene = true
script "wiki/ConSurf/hh/2hhd_consurf.spt"

consurf_color_levels.sptconsurf_color_levels.spt

This script is called by the [PDB code]_consurf.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 the consurf level terms ~con## have been defined beforehand.

# Any protein atoms not assigned a consurf level, e.g. short peptides not processed by consurf,
# will remain the following color. Example: chain P in 2VAA.
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]

consurf_prescript.sptconsurf_prescript.spt

This script is constant. That is, it is the same for all PDB files. It is required by [PDB code]_consurf.spt.

if (consurf_initial_scene)

  # Hide molecule
  script "/wiki/scripts/allRenderingsOff.spt";

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

endif

consurf_postscript.sptconsurf_postscript.spt

This script is constant. That is, it is the same for all PDB files. It is required by [PDB code]_consurf.spt.

if (consurf_initial_scene)

  # Spacefill all protein.
  select protein
  define ~consurf_to_color selected # color all protein
  spacefill

  # Give all protein a carbon-colored backbone.
  backbone 0.4
  color backbone [xc8c8c8]

  # Show nucleic as phosphorus-colored cartoon.
  select nucleic
  cartoon
  color cpk

endif

# Unconditionally color the ~consurf_to_color atoms.
script consurf_color_levels.spt

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. These terms, ~con##, are used in consurf_color_levels.spt.
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 produces the Evolutionary Conservation initial scene only if consurf_initial_scene is true. Therefore, consurf_initial_scene 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.

script consurf_prescript.spt

# If consurf_levels_defined is undefined, it is false.
if (!consurf_levels_defined)
  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

  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

  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

  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

  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

  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

  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

  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

  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

  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

  consurf_levels_defined = true

endif # if (!consurf_levels_defined)

script consurf_postscript.spt

SAT Color by Conservation ScriptSAT Color by Conservation Script

It is proposed that the Color dialog in the SAT will include a new option to color by Evolutionary Conservation. Here is the script proposed to accomplish this.

The script below works regardless of whether the conservation levels (~con##) have been previously defined; that is, it works regardless of whether the Evolutionary Conservation block has previously been opened.

This script is not "constant". It must be generated per PDB code (see last line of script below).

# This script applies conservation colors to the previously selected (currently selected) atoms.

# In case the user selected some non-protein atoms:
select selected and protein

define ~consurf_to_color selected

consurf_initial_scene = false

script "wiki/ConSurf/hh/2hhd_consurf.spt"