User: satsurae

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satsurae120
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6 years, 7 months ago
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7 years, 10 months ago
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Posts by satsurae

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Extracting Single Chains From A Pdb File Using Edpdb Module
... Thanks for the responses. I ended up emailing the author of the module and he directed to use his new project MDAnalysis http://code.google.com/p/mdanalysis/. It is fairly straight forward to install, but does have a number of prerequisites. Here is the solution for extracting a chain taken from htt ...
written 6.8 years ago by satsurae120
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Extracting Single Chains From A Pdb File Using Edpdb Module
... I am trying to extract individual chains from a pdb file using the edPDB module. In python I load the module then: >>> edPDB.xpdb.write_pdb(structure='1ES7.pdb',filename='1ES7_B2.pdb', chain='B') to which I get the following error: edPDB.write_pdb: INFO Setting the chain id for ALL ...
pdb python written 6.8 years ago by satsurae120
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Answer: A: Basics Of Systems Biology...
... Kitano is a pretty good authority on systems biology. And he has a very good writing style. Here is a basic overview which you may have already come across: http://www.sciencemag.org/cgi/content/full/295/5560/1662 EDIT: Bernhard Palsson is the principal author on this protocol for network constructi ...
written 7.5 years ago by satsurae120
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Comment: C: Syntax For Neighborsearch Module In Biopython
... Thanks very much for the reply. Basically, what I want to do is find the nearest neighbors to the ligand bound in a protein. I need to do this for quite a few (over 200 pdbs) hence i wanted to use a script. So in this test case, the ligand has a resseq=600 and the chain starts at resseq=307. Does th ...
written 7.5 years ago by satsurae120
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Syntax For Neighborsearch Module In Biopython
... Hi, I'm having trouble with using this module, more specifically the 'search' function. How do i get the atom list from a pdb file (is this using PDBParser)? How do I use it to find the nearest residues from the co-crystallized ligand? Cheers ...
pdb biopython parsing written 7.5 years ago by satsurae120 • updated 18 days ago by jma.bullock0
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Comment: C: Compare Two Protein Sequences Using Local Blast
... Scratch that! Got it working using the pretty well documented program parameters on the ncbi website: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/ ...
written 7.8 years ago by satsurae120
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Comment: C: Compare Two Protein Sequences Using Local Blast
... Hi guys, thanks for all the help. However, after using the above formatdb line, I get a fatal error saying that the database was not found when using the blastall code. I think there is a problem in the indexing of the fasta to a 'database'. I wouldn't have thought I would need to index both databas ...
written 7.8 years ago by satsurae120
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Comment: C: Compare Two Protein Sequences Using Local Blast
... Thanks very much for your help! ...
written 7.9 years ago by satsurae120
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Compare Two Protein Sequences Using Local Blast
... Hi, I have been given a task to compare the all the protein sequences of a strain of campylobacter with a strain of E.coli. I would like to do this locally using Biopython and the inbuilt Blast tools. However, I'm stuck on how to program this and what tools I should be using. If anybody could point ...
biopython blast written 7.9 years ago by satsurae120 • updated 4.0 years ago by Biostar ♦♦ 20

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