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tutorials:mali_tutorial [2012/03/22 12:35]
cuff 		tutorials:mali_tutorial [2015/09/22 15:07] (current)
hafsa [A Short Introduction to CATH and Gene3D]
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 Each level has a **CATH code** associated with it. Have a look at the following: Each level has a **CATH code** associated with it. Have a look at the following:
  
-{{:tutorials:cath_code.png|}}+{{:tutorials:class_3_screenshot.png|}}
  
 In this example, the CATH code for the domain 1tsrB00 is 2.60.40.720. The **2** refers to the class to which the domain belongs (mainly beta), the **2.60** refers to the architecture, the **2.60.40** refers to the actual fold (topology) the domain adopts and **2.60.40.720** is the homologous superfamily code. In this example, the CATH code for the domain 1tsrB00 is 2.60.40.720. The **2** refers to the class to which the domain belongs (mainly beta), the **2.60** refers to the architecture, the **2.60.40** refers to the actual fold (topology) the domain adopts and **2.60.40.720** is the homologous superfamily code.
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 Please then input 2pmaA into the **PDB/CATH domain code** field and press **Continue**.  You have now submitted a CATHEDRAL job on our server. You might find that the job takes a few minutes to complete. If this is the case, please keep refreshing the page every minute or so until the results are displayed. Please then input 2pmaA into the **PDB/CATH domain code** field and press **Continue**.  You have now submitted a CATHEDRAL job on our server. You might find that the job takes a few minutes to complete. If this is the case, please keep refreshing the page every minute or so until the results are displayed.
  
-Alternatively, if the results are taking too long, click the following link: [[http://www.cathdb.info/cgi-bin/CathedralServerResults.pl?sub_id=1186&access_key=5374b492e463c3f39df077b958c35a20|CATHEDRAL results]].+Alternatively, if the results are taking too long, click the following link: [[http://v3-4.cathdb.info/cgi-bin/CathedralServerResults.pl?sub_id=2628&access_key=0d25ad543068b5698a715193c0a034ca|CATHEDRAL results]].
  
 The results are sorted by a score calculated by the weighted average of, for example, normalised RMSD, percentage overlap, sequence identity and SSAP score, with those comparisons with the highest scores at the top of the page. The first result is the chain A of 2pma hitting itself, but the second is a different structure (2rspA00). You will notice that the domain IDs on the CATHEDRAL results page are hyperlinked  to their entries in CATH.  The results are sorted by a score calculated by the weighted average of, for example, normalised RMSD, percentage overlap, sequence identity and SSAP score, with those comparisons with the highest scores at the top of the page. The first result is the chain A of 2pma hitting itself, but the second is a different structure (2rspA00). You will notice that the domain IDs on the CATHEDRAL results page are hyperlinked  to their entries in CATH. 
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