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data_curation:domain_chopping_documentation:index [2023/09/29 14:35] vwaman |
data_curation:domain_chopping_documentation:index [2023/09/29 14:40] (current) vwaman |
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| Please note that it can take a few seconds for pages to be loaded due to database read/write processes. Please avoid clicking buttons multiple times if a page is still loading otherwise this can cause page errors. | Please note that it can take a few seconds for pages to be loaded due to database read/write processes. Please avoid clicking buttons multiple times if a page is still loading otherwise this can cause page errors. | ||
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| - | **RasMol setup** | ||
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| - | To view the putative domains suggested by each algorithm, RasMol needs to interpret the .rasscript file downloaded from the CATH DomChop pages. If you are using Windows, please create a .bat file containing the following: | ||
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| - | cd "c:\Program Files\RasWin" # <change to directory containing your RasMol program> | ||
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| - | raswin.exe script %1 | ||
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| - | Please then use this .bat file to open any RasMol files downloaded from the DomChop pages. | ||
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| - | If you are using Linux, please create a file called rasscript.com, containing the following (assuming that the RasMol application is in your $PATH): | ||
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| - | #!/bin/sh | ||
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| - | rasmol script "$1" | ||
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| - | Please then use this rasscript.com file to open any RasMol files downloaded from the DomChop pages. | ||
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| - | RasMol colouring issues for lowercase chain ids | ||
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| - | Please note that there is a known issue with RasMol where the domain colouring is not accurate for PDB chains whose ids are lowercase. In these cases, please use either the 3D View tool or download the Pymol script to view with Pymol. | ||
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| **Checking the literature** | **Checking the literature** | ||
| Line 68: | Line 44: | ||
| Superpositions | Superpositions | ||
| The CC superpositions comprise the new query chain aligned with the best-matching chain that has already been chopped in CATH. The darker colours represent the new query and the lighter colours represent the best-match in CATH. | The CC superpositions comprise the new query chain aligned with the best-matching chain that has already been chopped in CATH. The darker colours represent the new query and the lighter colours represent the best-match in CATH. | ||
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| 2. **CATHEDRAL** | 2. **CATHEDRAL** | ||
| Line 129: | Line 101: | ||
| http://update.cathdb.info/cgi-bin/DomChop.pl?chain_id=4uj8B | http://update.cathdb.info/cgi-bin/DomChop.pl?chain_id=4uj8B | ||
| - | 4uj8B | + | - 4uj8B |
| - | 4y25A | + | - 4y25A |
| - | 4znoB | + | - 4znoB |
| - | 5a57A | + | - 5a57A |
| - | 5a8jA | + | - 5a8jA |
| - | 5aoqA | + | - 5aoqA |
| - | 5axgA | + | - 5axgA |
| - | 5b04I | + | - 5b04I |
| - | 5c0xK | + | - 5c0xK |
| - | 5c14A | + | - 5c14A |
| - | 5c1fA | + | - 5c1fA |
| - | 5c1sA | + | - 5c1sA |
| - | 5c22C | + | - 5c22C |
| - | 5c2wD | + | - 5c2wD |
| - | 5c4nD | + | - 5c4nD |
| - | 5c6tA | + | - 5c6tA |
| - | 5cwwB | + | - 5cwwB |
| - | 5cylF | + | - 5cylF |
| - | 5cyxA | + | - 5cyxA |
| - | 5cz3A | + | - 5cz3A |
| - | 5dcpA | + | - 5dcpA |
| - | 5dcqF | + | - 5dcqF |
| - | 5dqrA | + | - 5dqrA |
| - | 5du3A | + | - 5du3A |
| - | 5fx0A | + | - 5fx0A |
| Chopping summary acronymns | Chopping summary acronymns | ||
| Line 205: | Line 177: | ||
| **Happy domain chopping !!!!** | **Happy domain chopping !!!!** | ||
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