Difference between revisions of "Lab Journal - Task 9 (PAH)"
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To check if a gap is included in a structure, we first downloaded the pdb file in text format from the [http://www.rcsb.org/pdb/explore/explore.do?structureId=1dmw pdb] website and then used following unix shell-commands: |
To check if a gap is included in a structure, we first downloaded the pdb file in text format from the [http://www.rcsb.org/pdb/explore/explore.do?structureId=1dmw pdb] website and then used following unix shell-commands: |
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... |
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| + | == SCWRL == |
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| + | Before generating the mutations with SCWRL, we first had to filter the sequence from the pdb file. Therefore, we used the repairPDB script with following command: |
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| + | /opt/SS12_Practical/scripts/repairPDB 1J8U.pdb -seq > 1J8U_seq.txt |
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| + | Afterwards, we had to change the upper letters to lower ones, except for the interesting mutations. For this purpose, we generated a python script: |
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| + | up2low.py |
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| + | ... |
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| + | Then, we can generate a mutation with SCWRL for each sequence file like shown below: |
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| + | /opt/SS12-Practical/scwrl4/Scwrl4 -i 1J8U.pdb -s 1J8U_seq_mut1.txt -o 1J8U_mut1.pdb |
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[[Category: Phenylketonuria 2013]] |
[[Category: Phenylketonuria 2013]] |
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Revision as of 16:40, 10 August 2013
structure selection
The information for the resolution, chain and the positions in PAH can be found on the UniProt entry P00439 itself. The R-factor for the proteins, can be found on the PDBsum entries and the pH values on the pdb entries in the method section.
To check if a gap is included in a structure, we first downloaded the pdb file in text format from the pdb website and then used following unix shell-commands:
...
SCWRL
Before generating the mutations with SCWRL, we first had to filter the sequence from the pdb file. Therefore, we used the repairPDB script with following command:
/opt/SS12_Practical/scripts/repairPDB 1J8U.pdb -seq > 1J8U_seq.txt
Afterwards, we had to change the upper letters to lower ones, except for the interesting mutations. For this purpose, we generated a python script: up2low.py ... Then, we can generate a mutation with SCWRL for each sequence file like shown below:
/opt/SS12-Practical/scwrl4/Scwrl4 -i 1J8U.pdb -s 1J8U_seq_mut1.txt -o 1J8U_mut1.pdb
