Karsten Theis: New page: Here is an example: ==List of figures: Lysozyme== ===Initial view=== script: https://proteopedia.org/wiki/scripts/37/376372/Overall/3.spt coords: https://proteopedia.org/cgi-bin/getfroz...

2020-06-27T18:06:52Z

New page: Here is an example: ==List of figures: Lysozyme== ===Initial view=== script: https://proteopedia.org/wiki/scripts/37/376372/Overall/3.spt coords: https://proteopedia.org/cgi-bin/getfroz...

New page

Here is an example:

==List of figures: Lysozyme==

===Initial view===
script: https://proteopedia.org/wiki/scripts/37/376372/Overall/3.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?2f267243b1cf263a27c03cd5ce051b66
<blockquote>Overview of the 1HEW structure. The trace of the protein chain is shown in rainbow colors with the alpha carbons as gray spheres labeled with the residue one letter code. The carbohydrate ligand is shown as ball and stick in CPK colors (carbon: gray, oxygen: red, nitrogen: blue).</blockquote>

===ribbon view===
script: https://proteopedia.org/wiki/scripts/37/376372/Secondary_structure/7.spt

coords: same as Initial view
<blockquote>Overview of the 1HEW secondary structure: Alpha Helices, 3-10 helix, Beta Strands, with loops in white and disulfide bonds in yellow. Arrow tips point towards the C-terminal end.</blockquote>

===colored by conservation===
script: https://proteopedia.org/wiki/ConSurf/he/1hew_consurf.spt
coords: none

===this hypothetical model===
script: https://proteopedia.org/wiki/scripts/37/376372/Hex_model/1.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?caa67c01c8140e2b3f7b60e4e749f1dd
<blockquote>1HEW with additional three sugars modeled into the active site.</blockquote>

===covalent intermediate===
script: https://proteopedia.org/wiki/scripts/37/376372/Covalent_intermediate/2.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?932c10afc4e1e94cdeab12d300cbb47b (always reloads)
<blockquote>Structure of the covalent enzyme intermediate. The active site residue Asp 52 and the carbohydrate are shown in CPK colors, with the 2FO-FC electron density within 1.5 A of these atoms as blue mesh. The backbone trace is shown in gold.</blockquote>

===product complex with five sugar units===
script: https://proteopedia.org/wiki/scripts/37/376372/Product_complex/6.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?09a5df19589b9b4571d13eef460f52bf
<blockquote>Comparison of covalent intermediate (1H6M) and product complex (2WAR), both for the almost inactive Glu35Gln mutant. Backbone in gold, with ligand in thick wireframe and side chains of active site residues 35 and 52 in thin wireframe. Fluorine is shown in green.</blockquote>
===Jmol commands: buttons etc===
====front view====
moveto 2.0 { 579 257 774 163.39} 120.0 0.0 0.0 {-0.33203837 20.866533 19.55904} 31.371292 {0 0 0} 0 0 0 3.0 0.0 0.0;
====side view====
moveto /* time, axisAngle */ 2.0 { -919 -290 -267 175.7} /* zoom, translation */ 120.0 0.0 0.0 /* center, rotationRadius */ {-0.33203837 20.866533 19.55904} 31.371292 /* navigation center, translation, depth */ {0 0 0} 0 0 0 /* cameraDepth, cameraX, cameraY */ 3.0 0.0 0.0;\n
====side view too====
moveto /* time, axisAngle */ 2.0 { -430 -10 903 146.05} /* zoom, translation */ 120.0 0.0 0.0 /* center, rotationRadius */ {-0.33203837 20.866533 19.55904} 31.371292 /* navigation center, translation, depth */ {0 0 0} 0 0 0 /* cameraDepth, cameraX, cameraY */ 3.0 0.0 0.0;
====active site====
moveto /* time, axisAngle */ 2.0 { 14 -997 -82 164.64} /* zoom, translation */ 615.28 0.0 0.0 /* center, rotationRadius */ {6.174519999999999 24.04584 25.138840000000002} 40.46755187629986 /* navigation center, translation, depth */ {0 0 0} 0 0 0 /* cameraDepth, cameraX, cameraY */ 3.0 0.0 0.0;
====active site too====
moveto /* time, axisAngle */ 2.0 { 311 -943 -118 125.09} /* zoom, translation */ 500.88 16.86 6.57 /* center, rotationRadius */ {5.804955513628509 21.50459857126935 17.894926846396874} 35.7306153511559 /* navigation center, translation, depth */ {0 0 0} 0 0 0 /* cameraDepth, cameraX, cameraY */ 3.0 0.0 0.0;
====wobble====
script http://proteopedia.org/wiki/images/7/76/Wobble.spt
====bobble====
script http://proteopedia.org/wiki/images/b/b9/Bobble2.spt
====Lysozyme====
script /scripts/37/376372/Overall/3.spt; hide water; set zshade off; spin off;
====☼====
select ligand; selectionHalos ON; delay 0.5;selectionHalos OFF;
====☼====
select 1.CA; selectionHalos ON; delay 0.5;selectionHalos OFF;
====☼====
select *.ca and 1; selectionhalos on;\ndelay 0.5;\nselect *.ca and 1-10; delay 0.3;\nselect *.ca and 5-15; delay 0.2;\nselect *.ca and 11-20; delay 0.1;\nselect *.ca and 15-25; delay 0.1;\nselect *.ca and 21-30; delay 0.1;\nselect *.ca and 25-35; delay 0.1;\nselect *.ca and 31-40; delay 0.1;\nselect *.ca and 35-45; delay 0.1;\nselect *.ca and 41-50; delay 0.1;\nselect *.ca and 45-55; delay 0.1;\nselect *.ca and 51-60; delay 0.1;\nselect *.ca and 55-65; delay 0.1;\nselect *.ca and 61-70; delay 0.1;\nselect *.ca and 65-75; delay 0.1;\nselect *.ca and 71-80; delay 0.1;\nselect *.ca and 75-85; delay 0.1;\nselect *.ca and 81-90; delay 0.1;\nselect *.ca and 85-95; delay 0.1;\nselect *.ca and 91-100; delay 0.1;\nselect *.ca and 101-110; delay 0.1;\nselect *.ca and 111-122; delay 0.1;\nselect *.ca and 122-127; delay 0.2;\nselect *.ca and 124-129; delay 0.3;\nselect *.ca and 129; delay 0.5;\nselectionhalos off;
====☼====
select 129.CA; selectionHalos ON; delay 0.5;selectionHalos OFF;
====☼====
select BONDS ({0:3}); wireframe 0.6; delay 0.5; wireframe 0.1
====☼====
select helix and *.CA; selectionHalos ON; delay 0.5;selectionHalos OFF;
====☼====
select sheet and *.CA; selectionHalos ON; delay 0.5;selectionHalos OFF;
====Hydrophobic residues====
select backbone or water; spacefill off; hide ligand or (sidechain and not (met, cys, ile, leu, val, phe, tyr, trp))
====hydrophilic residues and proline====
select backbone or water; spacefill off; hide ligand or (sidechain and (met, cys, ile, leu, val, phe, tyr, trp))
====water====
select backbone; spacefill on; select water; spacefill 1.0; display all
====Choice of====
* '''hydrophobic side chains''': hide (hidden and not sidechain) or (sidechain and not (met, cys, ile, leu, val, phe, tyr, trp))
* '''hydrophilic side chains''': hide (hidden and not sidechain) or (sidechain and (met, cys, ile, leu, val, phe, tyr, trp))
* '''all side chains''': display (displayed and not sidechain) or sidechain
====Choice of====
* '''colored by hydrophobiticity''': select sidechain; color magenta; select sidechain and (cys, met, ile, leu, val, phe, tyr, trp); color gray; set echo ID bla 80% 0%; echo \"hydrophobic\"; color echo gray; frank off; set echo ID bla2 0% 0%; echo \"hydrophilic\"; color echo magenta
* '''colored by charge''': select sidechain; color white; select sidechain and (asp, glu); color red; select sidechain and (lys, arg, his); color blue; set echo ID bla 80% 0%; echo \"positive\"; color echo blue; frank off; set echo ID bla2 0% 0%; echo \"negative\"; color echo red
* '''colored by conservation''': select sidechain; define ~consurf_to_do selected; define ~consurf_to_color selected; useFullScript = true; consurf_initial_scene = false; script /wiki/ConSurf/he/1hew_consurf.spt; set echo ID bla 80% 0%; echo \"conserved\"; color echo palevioletred; frank off; set echo ID bla2 0% 0%; echo \"variable\"; color echo darkturquoise
====[± backbone spacefill]====
if ({*.O and backbone and visible}.size\x3e0) {select backbone; spacefill off} else {select backbone; spacefill on}
====[± ligand]====
if ({ligand and hidden}.size\x3e0) {display displayed or ligand} else {hide ligand or hidden}
====[± water]====
if ({water and visible}.size\x3e0) {select water; spacefill off} else {select water; spacefill 1.0}
====hydrogen bonds====
set picking center; display all; script /scripts/37/376372/Hbonds/5.spt
====helices====
script /scripts/37/376372/Hbonds/1.spt; select helix and backbone; hbonds 0.2; delay 1.2; hbonds 0.04;
====beta turns====
script /scripts/37/376372/Hbonds/5.spt; select 74,77; hbonds 0.2; delay 1.2; hbonds 0.04;
====between strands====
script /scripts/37/376372/Hbonds/2.spt; select sheets and backbone; hbonds 0.2; delay 1.2; hbonds 0.04;
====Ordered waters====
hide none; script /scripts/37/376372/Hbonds/4.spt
====between protein and ligand====
script /scripts/37/376372/Hbonds/3.spt; select ligand and not 201:A.O1; set bondMode OR; hbonds 0.2; delay 1.2; hbonds 0.04;
====toggle fading and slabbing====
if (zshade) {set zshade off; slab off} else {set zshade on; slab on}
====turn centering on====
set picking center
====turn centering off====
set picking identify
====modeled extra sugars====
* '''[On]''': display all
* '''[Off]''': hide 204-206
====Choice of====
* '''product''': anim off; delay 1.0; model 1
* '''intermediate''': anim off; delay 1.0; model 2
* '''animate''': anim fps 1; anim mode loop; anim on;
====just ring====
* '''[On]''': hide ligand and not ((1134 or G2F) and (*.O1, *.C1, *.C2, *.C3, *.C4, *.C5, *.O5, *.N5, *.O4))
* '''[Off]''': hide water
===Summary===
Total of green links: 6

Total of Jmol buttons etc: 35
====coordinates used====
*1HEW: https://proteopedia.org/cgi-bin/getfrozenstructure?2f267243b1cf263a27c03cd5ce051b66
*do a manual check: https://proteopedia.org/cgi-bin/getfrozenstructure?caa67c01c8140e2b3f7b60e4e749f1dd
*1H6M: https://proteopedia.org/cgi-bin/getfrozenstructure?932c10afc4e1e94cdeab12d300cbb47b
*do a manual check: https://proteopedia.org/cgi-bin/getfrozenstructure?09a5df19589b9b4571d13eef460f52bf

User talk:Karsten Theis/Reviewing tools - Revision history

Karsten Theis: New page: Here is an example: ==List of figures: Lysozyme== ===Initial view=== script: https://proteopedia.org/wiki/scripts/37/376372/Overall/3.spt coords: https://proteopedia.org/cgi-bin/getfroz...