User:Eric Martz/Sandbox 3

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Contents

ConSurf Prototype

PDB ID 2hhd

Drag the structure with the mouse to rotate
2hhd, resolution 2.20Å ()
Ligands: ,
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.
  • The color key image should be centered (I could not get it centered in the mockup).
  • [✓] 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:

Evolutionary Conservation:                     [show]


After expanding, it could look like this:

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.

  1. All chains are colored and spacefilled, not just one chain. This includes both sequence-identical chains, and sequence different chains.
  2. The 10 color grade groups of residues are selected only once, for all chains, as shown in the example script below.
  3. 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

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Jaime Prilusky

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