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User:Karsten Theis/Electron density: Difference between revisions

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New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...
 
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==Your Heading Here (maybe something like 'Structure')==
<StructureSection size='500' side='right' caption='Caption for this structure' scene='79/790960/Dna/1'>
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Karsten Theis/Electron density'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.


== Function ==
To explore the electron density of the structure 233D (a short piece of DNA containing some sulfur-modified sugars), choose one of the two scenes below (either the entire molecule, or just a base pair. The latter will load faster and is less confusing, so maybe start with the base pair).


== Disease ==
<scene name='79/790960/Dna/1'>DNA</scene>


== Relevance ==
<scene name='79/790960/Bp/1'>Base pair</scene>


== Structural highlights ==
<scene name='79/790960/Water/1'>water (solvent)</scene>


This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
The following is the command to fetch the electron density from the pdbe.org database and display it around the selected atoms:
isosurface s_one sigma 1.0 color blue within 1.5 {selected} "http://www.ebi.ac.uk/pdbe/coordinates/files/233d.ccp4" mesh nofil


</StructureSection>
===Electron density===
== References ==
Click on the following buttons to display electron density at different contour levels. One sigma means to show the area (within the chicken wire) that has values higher than one standard deviation over the mean. The higher the sigma, the less density you see (but you get to see the highest peaks in the density).
<references/>
 
<jmol>
<jmolButton>
<script>isosurface s_one sigma 4.0 color blue within 1.5 {selected} "http://www.ebi.ac.uk/pdbe/coordinates/files/233d.ccp4" mesh nofill</script>
  <text>4 sigma</text>
</jmolButton>
</jmol>
The peaks are mostly around the phosphorous atoms. P has about twice as many electrons as C, N and O, so it is expected to have roughly twice the electron density (and, even more roughly, twice the maximum electron density at the center of the atom).
 
<jmol>
<jmolButton>
<script>isosurface s_one sigma 3.0 color blue within 1.5 {selected} "http://www.ebi.ac.uk/pdbe/coordinates/files/233d.ccp4" mesh nofill</script>
  <text>3 sigma</text>
</jmolButton>
</jmol>
At 3 sigma, you begin to see other parts of the structure when it is highly ordered. You also see the sulfur atoms, which are also third row elements.
 
<jmol>
<jmolButton>
<script>isosurface s_one sigma 1.5 color blue within 1.5 {selected} "http://www.ebi.ac.uk/pdbe/coordinates/files/233d.ccp4" mesh nofill</script>
  <text>1.5 sigma</text>
</jmolButton>
</jmol>
This is a good contour level for modelling. You can see evidence for most of the atoms, but the level of noise is not that bad.
 
<jmol>
<jmolButton>
<script>isosurface s_one sigma 1.0 color blue within 1.5 {selected} "http://www.ebi.ac.uk/pdbe/coordinates/files/233d.ccp4" mesh nofill</script>
  <text>1.0 sigma</text>
</jmolButton>
</jmol>
If you don't see your model at 1 sigma, you probably should not put in those atoms. At this level, you see a lot of solvent molecules and a lot of noise.
 
===A technical note===
This is not the most efficient way of displaying electron density, and it works because the structures displayed here are rather small. Every time you click on a button to display electron density, the entire electron density file is fetched from the database, and your browser has to read it all to find those points in space that are close to the selected atoms and have a density higher than the cutoff.
 
Update: there is now an efficient way to just fetch the part of the map you need:
 
isosurface within 3 {visible} "=233D"
 
will retrieve that part of the map within 3 Angstroem away from any atom displayed.
 
Try it:
 
<jmol>
<jmolButton>
<script>isosurface within 3 {visible} "=233D"</script>
  <text>faster way to a map</text>
</jmolButton>
</jmol>
 
If you already know what density you want to show, it is much faster (and saves space) to save the "chicken-wire" object as a .jvxl file and upload it to Proteopedia. These files are much smaller (especially if you are showing the density around just a couple of atoms, which is the typical case for publication figures). An example of this technique is explained [[Talk:Kisker_lab:_5B5Q|here]].
 
===Ferrodoxin: Ultra-high resolution===
 
<scene name='79/790960/Ferredoxin/1'>Ferredoxin</scene> is a small protein that binds to a certain metal.
 
For this structure, we can look at the density at very high contour level to find the metal.
 
<jmol>
<jmolButton>
<script>isosurface s_one sigma 20.0 color blue within 3.5 {selected} "http://www.ebi.ac.uk/pdbe/coordinates/files/1iqz.ccp4" mesh nofill</script>
  <text>20 sigma</text>
</jmolButton>
</jmol>
 
This will take long to load... the density file has a size of 11.2 Mbyte and your browser might ask you whether you want to continue. Once its loaded, see it you can spot the metals in the structure. To see the interpretation, click the button below.
 
<jmol>
<jmolButton>
<script>select not protein and not solvent; spacefill 20%; wireframe 30%</script>
  <text>show non-protein atoms</text>
</jmolButton>
</jmol>
 
If your patience did not run out, you can look at the density at the typical 1.5 sigma to see all atoms.
<jmol>
<jmolButton>
<script>isosurface s_two sigma 1.5 color silver within 3.5 {selected} "http://www.ebi.ac.uk/pdbe/coordinates/files/1iqz.ccp4" mesh nofill</script>
  <text>1.5 sigma</text>
</jmolButton>
</jmol>
 
===Pre-calculated density===
This is <scene name='79/790960/Ferredoxin_density/2'>Ferredoxin</scene>  again, surrounded by 20 sigma density. It loads faster because the density was rendered already and saved as a small file (10 kB instead of 11.2 Mb - factor 1000 less).
 
Even the 1.5 sigma density around <scene name='79/790960/Ferredoxin_density/3'>ferredoxin</scene>loads faster (222kB file). This is the kind of display you would use to build or rebuild an atomic model into electron density. To be able to see the trees in the forest, you use a technique called slabbing, illustrated below.
 
*<jmol>
<jmolLink>
  <script> slab on; depth 40; var a = [90,80,70,60,55,54,53,52,51]; for(var i IN a) {slab @i; delay 0.4;}
  </script>
  <text>Slab into center of molecule</text>
</jmolLink>
</jmol>
 
*<jmol>
<jmolLink>
  <script> slab on; depth 40; var a = [51,52,53,54,55,60,70,80,90,100]; for(var i IN a) {slab @i; delay 0.4;}
  </script>
  <text>Slab out of center</text>
</jmolLink>
</jmol>
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