Difference between revisions of "Lab Journal Hemochromatosis Task9"
(Created page with "=== mut_seq.py === <source lang="python> import copy seq="rllrshslhylfmgaseqdlglslfealgyvddqlfvfydhesrrveprtpwvssrissqmwlqlsqslkgwdhmftvdfwtimenhnhskeshtlqvilgcemqednstegywkygydg…") |
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| + | == 3D mutations with SCWRL4 == |
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| + | |||
| + | First, the wild type sequence was extracted from the FASTA entry of 1A6Z on rcsb.org. Then, using mut_seq.py, all mutant sequences were generated. |
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| + | The mutated structures were then generated with SCWRL4 using the following command |
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| + | Scwrl4 -i <1a6z chain A pdb file> -o <mutated pdb> -s <mutated sequence file> |
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| + | |||
=== mut_seq.py === |
=== mut_seq.py === |
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| − | <source lang="python> |
+ | <source lang="python"> |
import copy |
import copy |
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seq="rllrshslhylfmgaseqdlglslfealgyvddqlfvfydhesrrveprtpwvssrissqmwlqlsqslkgwdhmftvdfwtimenhnhskeshtlqvilgcemqednstegywkygydgqdhlefcpdtldwraaeprawptklewerhkirarqnraylerdcpaqlqqllelgrgvldqqvpplvkvthhvtssvttlrcralnyypqnitmkwlkdkqpmdakefepkdvlpngdgtyqgwitlavppgeeqrytcqvehpgldqpliviw" |
seq="rllrshslhylfmgaseqdlglslfealgyvddqlfvfydhesrrveprtpwvssrissqmwlqlsqslkgwdhmftvdfwtimenhnhskeshtlqvilgcemqednstegywkygydgqdhlefcpdtldwraaeprawptklewerhkirarqnraylerdcpaqlqqllelgrgvldqqvpplvkvthhvtssvttlrcralnyypqnitmkwlkdkqpmdakefepkdvlpngdgtyqgwitlavppgeeqrytcqvehpgldqpliviw" |
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fName= str(key) + mut[key] + ".seq" |
fName= str(key) + mut[key] + ".seq" |
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with open(fName,"w+") as f: |
with open(fName,"w+") as f: |
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| − | f.write("".join(mut_seq[3:])) |
+ | f.write("".join(mut_seq[3:])) #leave out first three residues because they are missing in the PDB structure |
Revision as of 17:13, 24 August 2013
3D mutations with SCWRL4
First, the wild type sequence was extracted from the FASTA entry of 1A6Z on rcsb.org. Then, using mut_seq.py, all mutant sequences were generated. The mutated structures were then generated with SCWRL4 using the following command
Scwrl4 -i <1a6z chain A pdb file> -o <mutated pdb> -s <mutated sequence file>
mut_seq.py
<source lang="python"> import copy seq="rllrshslhylfmgaseqdlglslfealgyvddqlfvfydhesrrveprtpwvssrissqmwlqlsqslkgwdhmftvdfwtimenhnhskeshtlqvilgcemqednstegywkygydgqdhlefcpdtldwraaeprawptklewerhkirarqnraylerdcpaqlqqllelgrgvldqqvpplvkvthhvtssvttlrcralnyypqnitmkwlkdkqpmdakefepkdvlpngdgtyqgwitlavppgeeqrytcqvehpgldqpliviw" seq= list(seq)
mut = {53:"M",63:"D",97:"I",217:"I",282:"Y"}
for key in mut.iterkeys(): mut_seq = copy.deepcopy(seq) mut_seq[key-23] = mut[key] ## -(22+1) 22 for PDB - seq offset and 1 for indexing starting at 0 fName= str(key) + mut[key] + ".seq" with open(fName,"w+") as f: f.write("".join(mut_seq[3:])) #leave out first three residues because they are missing in the PDB structure
</source>
