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Update documentation
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mpavsic committed Feb 21, 2024
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10 changes: 5 additions & 5 deletions _sources/strukture/prim.md
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Expand Up @@ -8,7 +8,7 @@
:::{grid-item}
```{image} ../seje/ak-abeceda.png
:name: ak-abeceda
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/ak-abeceda.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/ak-abeceda.molx&snapshot-url-type=molx&hide-controls=1
```
:::
Expand All @@ -19,7 +19,7 @@ V seji je peptid z aminokislinskim zaporedjem GASTCDNEQHPLIVMKRFYW (torej vseh 2
:::
::::
Za ogled je na voljo tudi [seja](https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/ak-abeceda_H.molx&snapshot-url-type=molx&hide-controls=1), kjer so prikazani in označeni vodikovi atomi. Bodite pozorni na protonacijsko stanje N- ter C-konca in aspartatnega, glutamatnega, argininskega, lizinskega in histidinskega ostanka.
Za ogled je na voljo tudi [seja](https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/ak-abeceda_H.molx&snapshot-url-type=molx&hide-controls=1), kjer so prikazani in označeni vodikovi atomi. Bodite pozorni na protonacijsko stanje N- ter C-konca in aspartatnega, glutamatnega, argininskega, lizinskega in histidinskega ostanka.
(tabela-grske-latinske-oznake)=
**Tabela pretvorb iz grških v latinske oznake**
Expand All @@ -39,7 +39,7 @@ Za ogled je na voljo tudi [seja](https://molstar.org/viewer/?snapshot-url=https:
```{dropdown} Povezave
```{image} ../seje/ak-abeceda-qr.png
:width: 200px
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/ak-abeceda.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/ak-abeceda.molx&snapshot-url-type=molx&hide-controls=1
```
````

Expand All @@ -51,7 +51,7 @@ Za ogled je na voljo tudi [seja](https://molstar.org/viewer/?snapshot-url=https:
:::{grid-item}
```{image} ../seje/ak-D-ak.png
:name: vijacnica-beta-2
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/ak-D-ak.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/ak-D-ak.molx&snapshot-url-type=molx&hide-controls=1
```
:::
Expand All @@ -67,7 +67,7 @@ Nekateri peptidi in proteini vsebujejo D-aminokislinske ostanke, ki so lahko klj
```{dropdown} Povezave
```{image} ../seje/ak-D-ak-qr.png
:width: 200px
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/ak-D-ak.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/ak-D-ak.molx&snapshot-url-type=molx&hide-controls=1
```
````

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24 changes: 12 additions & 12 deletions _sources/strukture/ss.md
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Expand Up @@ -11,7 +11,7 @@ Sekundarna struktura je takoj nad primarno (aminokislinsko zaporedje) – gre za
:::{grid-item}
```{image} ../seje/vijacnica-alfa-desna-leva.png
:name: vijacnica-alfa-desna-leva
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vijacnica-alfa-desna-leva.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vijacnica-alfa-desna-leva.molx&snapshot-url-type=molx&hide-controls=1
```
:::
Expand All @@ -23,7 +23,7 @@ V naravnih proteinih prevladujejo desne $\alpha$ vijačnice. Občasno najdemo (p
```{dropdown} Povezave
```{image} ../seje/vijacnica-alfa-desna-leva-qr.png
:width: 200px
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vijacnica-alfa-desna-leva.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vijacnica-alfa-desna-leva.molx&snapshot-url-type=molx&hide-controls=1
```
````

Expand All @@ -36,7 +36,7 @@ V naravnih proteinih prevladujejo desne $\alpha$ vijačnice. Občasno najdemo (p
:::{grid-item}
```{image} ../seje/vijacnica-310.png
:name: vijacnica-310
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vijacnica-310.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vijacnica-310.molx&snapshot-url-type=molx&hide-controls=1
```
:::
Expand All @@ -48,7 +48,7 @@ $3_{10}$ vijačnice so ponavadi kratke, lahko se nahajajo na začetku ali koncu
```{dropdown} Povezave
```{image} ../seje/vijacnica-310-qr.png
:width: 200px
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vijacnica-310.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vijacnica-310.molx&snapshot-url-type=molx&hide-controls=1
```
````

Expand All @@ -60,7 +60,7 @@ $3_{10}$ vijačnice so ponavadi kratke, lahko se nahajajo na začetku ali koncu
:::{grid-item}
```{image} ../seje/vijacnica-310-sinteticna.png
:name: vijacnica-310-sinteticna
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vijacnica-310-sinteticna.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vijacnica-310-sinteticna.molx&snapshot-url-type=molx&hide-controls=1
```
:::
Expand All @@ -72,7 +72,7 @@ V naravi najdemo daljše $3_{10}$ vijačnice le izjemoma, lahko pa jih ustvarimo
```{dropdown} Povezave
```{image} ../seje/vijacnica-310-sinteticna-qr.png
:width: 200px
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vijacnica-310-sinteticna.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vijacnica-310-sinteticna.molx&snapshot-url-type=molx&hide-controls=1
```
````

Expand All @@ -85,7 +85,7 @@ V naravi najdemo daljše $3_{10}$ vijačnice le izjemoma, lahko pa jih ustvarimo
:::{grid-item}
```{image} ../seje/vijacnica-pi-aktivno_mesto.png
:name: vijacnica-pi-aktivno_mesto
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vijacnica-pi-aktivno_mesto.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vijacnica-pi-aktivno_mesto.molx&snapshot-url-type=molx&hide-controls=1
```
:::
Expand All @@ -97,7 +97,7 @@ Primer, ko je insercija aminokislinskega ostanka vodila do nastanka $\pi$ vijač
```{dropdown} Povezave
```{image} ../seje/vijacnica-pi-aktivno_mesto-qr.png
:width: 200px
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vijacnica-pi-aktivno_mesto.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vijacnica-pi-aktivno_mesto.molx&snapshot-url-type=molx&hide-controls=1
```
````

Expand All @@ -109,7 +109,7 @@ Primer, ko je insercija aminokislinskega ostanka vodila do nastanka $\pi$ vijač
:::{grid-item}
```{image} ../seje/vijacnica-beta.png
:name: vijacnica-beta
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vijacnica-beta.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vijacnica-beta.molx&snapshot-url-type=molx&hide-controls=1
```
:::
Expand All @@ -121,7 +121,7 @@ Ena izmed oblik $\beta$ vijačnice je struktura, ki jo tvori polipeptidna veriga
```{dropdown} Povezave
```{image} ../seje/vijacnica-beta-qr.png
:width: 200px
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vijacnica-beta.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vijacnica-beta.molx&snapshot-url-type=molx&hide-controls=1
```
````

Expand All @@ -133,7 +133,7 @@ Ena izmed oblik $\beta$ vijačnice je struktura, ki jo tvori polipeptidna veriga
:::{grid-item}
```{image} ../seje/vijacnica-beta-2.png
:name: vijacnica-beta-2
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vijacnica-beta.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vijacnica-beta-2.molx&snapshot-url-type=molx&hide-controls=1
```
:::
Expand All @@ -145,6 +145,6 @@ Drug primer $\beta$ vijačnic so strukture, sestavljene iz kratkih $\beta$ trako
```{dropdown} Povezave
```{image} ../seje/vijacnica-beta-2-qr.png
:width: 200px
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vijacnica-beta.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vijacnica-beta-2.molx&snapshot-url-type=molx&hide-controls=1
```
````
4 changes: 2 additions & 2 deletions _sources/strukture/vizualizacija.md
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Expand Up @@ -8,7 +8,7 @@
:::{grid-item}
```{image} ../seje/vizualizacija-nacini_prikaza.png
:name: vizualizacija-nacini_prikaza
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vizualizacija-nacini_prikaza.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vizualizacija-nacini_prikaza.molx&snapshot-url-type=molx&hide-controls=1
```
:::
Expand All @@ -30,6 +30,6 @@ Za vse, ki jih zanima zgodovina (in sedanjost) področja vizualizacije makromole
```{dropdown} Povezave
```{image} ../seje/vizualizacija-nacini_prikaza-qr.png
:width: 200px
:target: https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/vizualizacija-nacini_prikaza.molx&snapshot-url-type=molx&hide-controls=1
:target: https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/vizualizacija-nacini_prikaza.molx&snapshot-url-type=molx&hide-controls=1
```
````
10 changes: 5 additions & 5 deletions strukture/prim.html
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Expand Up @@ -367,15 +367,15 @@ <h1>Primarna struktura<a class="headerlink" href="#primarna-struktura" title="Li
<div class="sd-container-fluid sd-sphinx-override sd-mb-4 docutils">
<div class="sd-row sd-row-cols-1 sd-row-cols-xs-1 sd-row-cols-sm-1 sd-row-cols-md-2 sd-row-cols-lg-2 sd-flex-row-reverse docutils">
<div class="sd-col sd-d-flex-column docutils">
<a class="reference external image-reference" href="https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/ak-abeceda.molx&amp;snapshot-url-type=molx&amp;hide-controls=1"><img alt="../_images/ak-abeceda.png" id="ak-abeceda" src="../_images/ak-abeceda.png" /></a>
<a class="reference external image-reference" href="https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/ak-abeceda.molx&amp;snapshot-url-type=molx&amp;hide-controls=1"><img alt="../_images/ak-abeceda.png" id="ak-abeceda" src="../_images/ak-abeceda.png" /></a>
</div>
<div class="sd-col sd-d-flex-column docutils">
<p class="sd-card-text">Elementnim oznakam atomov aminokislin(skih ostankov) po dogovoru dodajamo majhne črke grške abecede začenpi z <span class="math notranslate nohighlight">\(\alpha\)</span> ter eventuelno še arabske številke, s čimer vsak atom dobi unikatno oznako. Programi za vizualizacijo grške črke ponavadi pretvorijo kar v latinske in na tak način so atomi označeni tudi v datotekah PDB in (mm)CIF – pri tem npr. <span class="math notranslate nohighlight">\(\alpha\)</span> postane A itd. (vse pretvorbe so zbrane v <a class="reference internal" href="#tabela-grske-latinske-oznake"><span class="std std-ref">tabeli</span></a>).</p>
<p class="sd-card-text">V seji je peptid z aminokislinskim zaporedjem GASTCDNEQHPLIVMKRFYW (torej vseh 20 standarnih aminokislinskih ostankov), kjer so atomi označeni v skladu z zgoraj omenjeno nomenklaturo.</p>
</div>
</div>
</div>
<p class="sd-card-text">Za ogled je na voljo tudi <a class="reference external" href="https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/ak-abeceda_H.molx&amp;amp;snapshot-url-type=molx&amp;amp;hide-controls=1">seja</a>, kjer so prikazani in označeni vodikovi atomi. Bodite pozorni na protonacijsko stanje N- ter C-konca in aspartatnega, glutamatnega, argininskega, lizinskega in histidinskega ostanka.</p>
<p class="sd-card-text">Za ogled je na voljo tudi <a class="reference external" href="https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/ak-abeceda_H.molx&amp;amp;snapshot-url-type=molx&amp;amp;hide-controls=1">seja</a>, kjer so prikazani in označeni vodikovi atomi. Bodite pozorni na protonacijsko stanje N- ter C-konca in aspartatnega, glutamatnega, argininskega, lizinskega in histidinskega ostanka.</p>
<p class="sd-card-text" id="tabela-grske-latinske-oznake"><strong>Tabela pretvorb iz grških v latinske oznake</strong></p>
<table class="table">
<thead>
Expand Down Expand Up @@ -430,7 +430,7 @@ <h1>Primarna struktura<a class="headerlink" href="#primarna-struktura" title="Li
<div class="sd-summary-up docutils">
<svg version="1.1" width="1.5em" height="1.5em" class="sd-octicon sd-octicon-chevron-up" viewBox="0 0 24 24" aria-hidden="true"><path fill-rule="evenodd" d="M18.78 15.28a.75.75 0 000-1.06l-6.25-6.25a.75.75 0 00-1.06 0l-6.25 6.25a.75.75 0 101.06 1.06L12 9.56l5.72 5.72a.75.75 0 001.06 0z"></path></svg></div>
</summary><div class="sd-summary-content sd-card-body docutils">
<a class="reference external image-reference" href="https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/ak-abeceda.molx&amp;snapshot-url-type=molx&amp;hide-controls=1"><img alt="../_images/ak-abeceda-qr.png" src="../_images/ak-abeceda-qr.png" style="width: 200px;" /></a>
<a class="reference external image-reference" href="https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/ak-abeceda.molx&amp;snapshot-url-type=molx&amp;hide-controls=1"><img alt="../_images/ak-abeceda-qr.png" src="../_images/ak-abeceda-qr.png" style="width: 200px;" /></a>
</div>
</details></div>
</div>
Expand All @@ -441,7 +441,7 @@ <h1>Primarna struktura<a class="headerlink" href="#primarna-struktura" title="Li
<div class="sd-container-fluid sd-sphinx-override sd-mb-4 docutils">
<div class="sd-row sd-row-cols-1 sd-row-cols-xs-1 sd-row-cols-sm-1 sd-row-cols-md-2 sd-row-cols-lg-2 sd-flex-row-reverse docutils">
<div class="sd-col sd-d-flex-column docutils">
<a class="reference external image-reference" href="https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/ak-D-ak.molx&amp;snapshot-url-type=molx&amp;hide-controls=1"><img alt="../_images/ak-D-ak.png" id="vijacnica-beta-2" src="../_images/ak-D-ak.png" /></a>
<a class="reference external image-reference" href="https://molstar.org/viewer/?snapshot-url=https://raw.githubusercontent.com/mpavsic/sbio/main/sbio/seje/ak-D-ak.molx&amp;snapshot-url-type=molx&amp;hide-controls=1"><img alt="../_images/ak-D-ak.png" id="vijacnica-beta-2" src="../_images/ak-D-ak.png" /></a>
</div>
<div class="sd-col sd-d-flex-column docutils">
<p class="sd-card-text">Nekateri peptidi in proteini vsebujejo D-aminokislinske ostanke, ki so lahko ključni za samo strukturo, hkrati pa pogosto omogočajo odpornost peptidne vezi, v kateri so udeleženi, na “napad” s strani peptidaz, ki so večinoma prilagojene za hidrolizo peptidnih vezi med L-aminokislinskimi ostanki. Primer je antibiotik gramicidin A iz <em>Bacillus brevis</em> (PDB <a class="reference external" href="https://www.rcsb.org/structure/1BDW">1BDW</a>), pri katerem si alternirajoče sledijo D- in L-aminokislinski ostanki.</p>
Expand All @@ -459,7 +459,7 @@ <h1>Primarna struktura<a class="headerlink" href="#primarna-struktura" title="Li
<div class="sd-summary-up docutils">
<svg version="1.1" width="1.5em" height="1.5em" class="sd-octicon sd-octicon-chevron-up" viewBox="0 0 24 24" aria-hidden="true"><path fill-rule="evenodd" d="M18.78 15.28a.75.75 0 000-1.06l-6.25-6.25a.75.75 0 00-1.06 0l-6.25 6.25a.75.75 0 101.06 1.06L12 9.56l5.72 5.72a.75.75 0 001.06 0z"></path></svg></div>
</summary><div class="sd-summary-content sd-card-body docutils">
<a class="reference external image-reference" href="https://molstar.org/viewer/?snapshot-url=https://github.com/mpavsic/sbio/blob/main/sbio/seje/ak-D-ak.molx&amp;snapshot-url-type=molx&amp;hide-controls=1"><img alt="../_images/ak-D-ak-qr.png" src="../_images/ak-D-ak-qr.png" style="width: 200px;" /></a>
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