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==ConSurf Prototype==
==Notes on mini- and microproteins==


{{STRUCTURE_2hhd|  PDB=2hhd  |  SCENE= }}
===Micro===


===Scenes===
*2018: Microproteins are "translated from protein-coding small open reading frames (smORFs, less than 100–150 codons in length)." "to reduce false positives... most genome annotation pipelines required ORFs to be at least 300 nucleotides long (i.e. 100 amino acids) resulting in most smORFs being missed." <ref>PMID: 30415582</ref>
Opening the proposed <i>Evolutionary Conservation</i> 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:
*<scene name='User:Eric_Martz/Sandbox_3/Consurf/1'>ConSurf color all 4 chains</scene> (2 alphas, A and C, and 2 betas, B and D, in 2HHD).
*<scene name='User:Eric_Martz/Sandbox_3/Consurf/2'>ConSurf color only chains A and B</scene> (one alpha, one beta)
*<scene name='User:Eric_Martz/Sandbox_3/Consurf/3'>ConSurf color only chains A and C</scene> (both alphas)
*<scene name='User:Eric_Martz/Sandbox_3/Consurf/4'>ConSurf color only chain A</scene>
*<scene name='User:Eric_Martz/Sandbox_3/Consurf/5'>All chains unchecked</scene>


===Button Tests===
*2015: "MicroProteins (miPs) are short, usually single-domain proteins that, in analogy to miRNAs, heterodimerize with their targets and exert a dominant-negative effect." They "disrupt the formation of homodimeric, heterodimeric, or multimeric complexes". "The term ‘microProtein’ was coined due to their small size and negative regulatory similarity to miRNAs" <ref>PMID: 26115780</ref>


<!-- UNNECESSARY WITH REVISED IF LOGIC
<jmol>
<jmolButton>
<script> ~A = 1;~B = 1;</script>
<text>set A, B</text>
</jmolButton>
</jmol>
-->


<jmol>
*2011 review <ref>PMID: 21151039</ref>
<jmolButton>
<script>if (consurf_A!=0); select:A; spacefill off;color translucent -1; consurf_A = 0;javascript "document.getElementById('jmb_A').value='A [  ]'"; else; select:A; spacefill on; color opaque;consurf_A = 1;javascript "document.getElementById('jmb_A').value='A [x]';"; endif;</script>
<text>A [  ]</text>
<name>jmb_A</name>
</jmolButton>
</jmol> 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
===Mini===
*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).


<!--
*2017: Miniproteins are "polypeptide chains <40 amino acids in length that adopt defined and stable 3D structures". They are often designed, or screened from designed libraries. <ref>PMID: 28832117</ref>
Checkmark is &#10003;
<jmol>
<jmolButton>
<script>if (~B==1); select:B; spacefill off;color translucent -1; ~B = 0;javascript "bB.value='B[  ]'"; else; select:B; spacefill on; color opaque;~B = 1;javascript "bB.value='B[x]'"; endif;</script>
<text>\B\[✓\]</text>
<name>bB</name>
</jmolButton>
</jmol> The checkmark causes the previous characters to disappear. ??
-->


<jmol>
*2017: De novo designed: <ref>PMID: 28953867</ref>
<jmolButton>
<script>if (~B!=0); select:B; spacefill off;color translucent -1; ~B = 0;javascript "bB.value='B [  ]'"; else; select:B; spacefill on; color opaque;~B = 1;javascript "bB.value='B [x]'"; endif;</script>
<text>B [  ]</text>
<name>bB</name>
</jmolButton>
</jmol> 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: &#10003; but if it is used in the button text label, the previous characters don't appear. Could maybe use a button label &#10003;A instead of A[&#10003;], 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.)
*2015: Viruses have hydrophobic, membrane-spanning miniproteins. <ref>PMID: 26057606</ref> <ref>PMID: 24742054</ref>


===User Interface & Color Key===
*2011: Cysteine knot miniproteins are a subset of miniproteins that can be natural or engineered. <ref>PMID: 22204431</ref>


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 <i>Complete results at ConSurf</i> will provide a path to the display in <i>FirstGlance in Jmol</i> with many more options.
==In Proteopedia==
*There are about 60 entries found with a search for "miniprotein" (but no such category).
*[[:Category:Microprotein]] has 3 entries, and [[:Category:Hybrid microprotein]] has 1.


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]].


 
==References==
<b>Before expanding this section, it could look like this:</b>
<references />
 
<table border="0" cellspacing="0" cellpadding="2" width="330">
<tr>
<td align="left" colspan="2" bgcolor="#bac9f7">
<font color="#2020e0"><b>Evolutionary Conservation:</b></font>
&nbsp; &nbsp; &nbsp; &nbsp;
&nbsp; &nbsp; &nbsp; &nbsp;
&nbsp; &nbsp;
[<font color="#1010ff">show</font>]
</td></tr>
</table>
 
<br>
 
<b>After expanding, it could look like this (using buttons):</b>
<table class="collapsible collapsed" border="0" cellspacing="0" width="330">
<tr>
<td align="left" colspan="2" bgcolor="#bac9f7">
<font color="#2020e0"><b>Evolutionary Conservation:</b></font>
&nbsp; &nbsp; &nbsp; &nbsp;
&nbsp; &nbsp; &nbsp; &nbsp;
&nbsp; &nbsp; &nbsp;
[<font color="#1010ff">hide</font>]
</td></tr>
<tr><td colspan="2" style="background-color:#bac9f7;color:#040d44;vertical-align:top;text-align:left;"></td></tr>
<!-- <tr><td colspan='2'  style="background-color:#bac9f7;"> -->
<tr><td colspan='2'  style="background-color:#bac9f7;">
[[Image:Consurf_key_small.gif|center]]
</td></tr>
 
<tr><td style="background-color:#bac9f7;color:#040d44;vertical-align:top;text-align:left;">
<b>Toggle Conservation Colors:</b>
</td><td align="left" style="background-color:#ace3ac;border-top:2px solid #dddddd; border-right:2px solid #dddddd" width="230">&nbsp;Rows = identical sequences:<br>
<jmol>
<jmolButton>
<script>if (consurf_A!=0); select:A; spacefill off;color translucent -1; consurf_A = 0;javascript "document.getElementById('jmb_AA').value='A [  ]'"; else; select:A; spacefill on; color opaque;consurf_A = 1;javascript "document.getElementById('jmb_AA').value='A [x]';"; endif;</script>
<text>A [  ]</text>
<name>jmb_AA</name>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>if (consurf_C!=0); select:C; spacefill off;color translucent -1; consurf_C = 0;javascript "document.getElementById('jmb_C').value='C [  ]'"; else; select:C; spacefill on; color opaque;consurf_C = 1;javascript "document.getElementById('jmb_C').value='C [x]';"; endif;</script>
<text>C [  ]</text>
<name>jmb_C</name>
</jmolButton>
</jmol>
<hr noshade>
<jmol>
<jmolButton>
<script>javascript "alert('Not implemented in mockup.')"</script>
<text>B [  ]</text>
<name>jmb_BB</name>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>javascript "alert('Not implemented in mockup.')"</script>
<text>D [  ]</text>
<name>jmb_D</name>
</jmolButton>
</jmol>
</td></tr>
 
<tr><td style="background-color:#bac9f7;color:#040d44;vertical-align:top;text-align:left;"> <b>Further Information:</b>
</td><td align="left" style="background-color:#ace3ac;border-top:2px solid #dddddd; border-right:2px solid #dddddd" width="230">
<font color="#2020e0">Explanation
<br><br>
Complete results at ConSurf</font>
</td></tr>
 
</table>
 
<!--
<br>
<b>After expanding, it could look like this (using green links):</b>
<table class="collapsible collapsed" border="0" cellspacing="0" width="330">
<tr>
<td align="left" colspan="2" bgcolor="#bac9f7">
<font color="#2020e0"><b>Evolutionary Conservation:</b></font>
&nbsp; &nbsp; &nbsp; &nbsp;
&nbsp; &nbsp; &nbsp; &nbsp;
&nbsp; &nbsp; &nbsp;
[<font color="#1010ff">hide</font>]
</td></tr>
<tr><td colspan="2" style="background-color:#bac9f7;color:#040d44;vertical-align:top;text-align:left;"></td></tr>
<tr><td colspan='2'  style="background-color:#bac9f7;">
[[Image:Consurf_key_small.gif|center]]
</td></tr>
 
<tr><td style="background-color:#bac9f7;color:#040d44;vertical-align:top;text-align:left;">
&nbsp;</td><td align="left" style="background-color:#ace3ac;border-top:2px solid #dddddd; border-right:2px solid #dddddd" width="230">
<font color="#009000"><b>Hide all conservation colors.</b></font>
</td></tr><tr><td style="background-color:#bac9f7;color:#040d44;vertical-align:top;text-align:left;">
<b>Click Chain(s) to Show Conservation:</b>
</td><td align="left" style="background-color:#ace3ac;border-top:2px solid #dddddd; border-right:2px solid #dddddd" width="230">&nbsp;Rows = identical sequences:<br>
<font color="#009000"><b>A C<br>B D</b></font>
</td></tr>
 
<tr><td style="background-color:#bac9f7;color:#040d44;vertical-align:top;text-align:left;"> <b>Further Information:</b>
</td><td align="left" style="background-color:#ace3ac;border-top:2px solid #dddddd; border-right:2px solid #dddddd" width="230">
<font color="#2020e0">Explanation
<br><br>
Complete results at ConSurf</font>
</td></tr>
 
</table>
-->
 
==Scripts==
When the <i>Evolutionary Conservation</i> block is expanded, a master script is run that colors and spacefills all chains.
<!--
Importantly, it also defines 10 groups of residues, to be colored as <i>insufficient data</i> (~con10), and grades 1-9 (conserved - variable, ~con1, ~con2, ..., ~con9). These terms greatly simplify the script needed when a checkbox is changed.
-->
 
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 Checkbox===
After a chain checkbox (in the expanded Evolutionary Conservation block) is changed, the currently checked chains are put into this script:
 
<tt><pre>select protein
spacefill off
select (:a,:c) # LIST OF CHECKED CHAINS
spacefill
</pre></tt>
 
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 Scripts===
 
[http://consurfdb.tau.ac.il 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 Script===
 
This is the script sent to Jmol when the ''Evolutionary Conservation'' block is expanded.
 
<tt><pre>
select protein
define ~consurf_to_do selected
consurf_initial_scene = true
script "/wiki/ConSurf/hh/2hhd_consurf.spt";
</pre></tt>
 
===consurf_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 <b>~consurf_to_color</b> be defined beforehand. It also requires that the consurf level terms ~con## have been defined beforehand.
 
<tt><pre>
# 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]
</pre></tt>
 
===consurf_prescript.spt===
This script is constant. That is, it is the same for all PDB files. It is required by [PDB code]_consurf.spt.
 
<tt><pre>
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
</pre></tt>
 
===consurf_postscript.spt===
This script is constant. That is, it is the same for all PDB files. It is required by [PDB code]_consurf.spt.
 
<tt><pre>
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 "/wiki/scripts/consurf_color_levels.spt";
 
</pre></tt>
 
===2hhd_consurf.spt===
 
# 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 <b>consurf_levels_defined</b>). 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.
# This script applies ConSurf colors to the protein atoms included in <b>~consurf_to_color</b> (which must therefore be defined before calling this script).
# This script produces the ''Evolutionary Conservation'' initial scene only if <b>consurf_initial_scene</b> is true. Therefore, <b>consurf_initial_scene</b> must be set before calling this script.
# Wherever possible, this script calls other scripts to separate commands that are not PDB-ID specific, so they can be maintained separately.
 
<tt><pre>
script "/wiki/scripts/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 "/wiki/scripts/consurf_postscript.spt";
 
</pre></tt>
 
===SAT 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).
 
<tt><pre>
# 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";
</pre></tt>
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