User: Felix_Sim

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Felix_Sim250
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2 years, 8 months ago
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6 years, 5 months ago
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Posts by Felix_Sim

<prev • 32 results • page 1 of 4 • next >
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Answer: A: kegg biopython error in retrieving enzyme record
... **This issue has been reported to the Biopython community on GitHub and the status can be monitored under issue [#1275](https://github.com/biopython/biopython/issues/1275).** > Update: > > This issue has in fact been resolved in Biopython v1.69, so run `pip > install -U biopython` and ...
written 3.0 years ago by Felix_Sim250
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Answer: A: Pymol Scripting Help
... **In my experience, you have two different approaches to your problem.** --- **1. PyMOL .pml script** This type contains basically a set of commands, just like you would manually type in a running PyMOL session, to read, write and manipulate structure objects. Typically, these files have the ``.p ...
written 3.9 years ago by Felix_Sim250
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Comment: C: Problem In running Modeller for Homology Modelling of Protein
... Is the model_default.py script in the same folder from which you invoke mod9.16? How did you install modeller? ...
written 4.0 years ago by Felix_Sim250
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Answer: A: T Coffee Commandline in Biopython
... Currently, the `TCoffeeCommandline` wrapper does not support the comparison of sequence alignments. According to the source code and documentation, it can only align sequences from a single sequence file. I.e., if you have 10 sequences in `unaligned.fasta`, you can align those sequences using the wr ...
written 4.0 years ago by Felix_Sim250
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Answer: A: Fragments for proteins with known structure for use in Rosetta
... Submitting to the Robetta server is generally not a problem. You might be in the queue for a few hours but the submission restriction to a maximum of 2 at the same time will get your fragments to be generated quite quickly. Using the server for a protein of interest is really the easiest route in my ...
written 4.0 years ago by Felix_Sim250
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Comment: C: Python Programming (Suggestions are needed)
... Have a look at "Learn Python The Hard Way". Really useful and good introduction to Python programming. ...
written 4.3 years ago by Felix_Sim250
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Answer: A: Python: Optimizing my amino acid % composition code
... I would substitute all the individual amino acid processing lines with loops or functions (as suggested by Ram). countC = singleletterstring.count('C') countD = singleletterstring.count('D') countS = singleletterstring.count('S') countQ = singleletterstring.count('Q') countK = s ...
written 4.3 years ago by Felix_Sim250 • updated 4 months ago by RamRS27k
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Answer: A: Biopython SeqIO: remove gene annotation if not in a list from GenBank file
... I'm unable to test this implementation right now but maybe something along the following lines: from Bio import SeqIO input = 'test.gbk' keep = ['gene1', 'gene2', 'gene3', 'gene4'] with open(input, 'rU') as input: for record in SeqIO.parse(input, 'genbank'): for index, feature in enume ...
written 4.4 years ago by Felix_Sim250
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Answer: A: PDB rotation along parallel axis using biopython
... I have attempted to solve your problem; although, your question did not provide me with a lot of information. The following code reads a pdb structure (1eaz in this case) and rotates it 90 degrees around your provided vector. ``` from Bio.PDB import * import numpy # Parse the structure file struc ...
written 4.4 years ago by Felix_Sim250 • updated 8 months ago by RamRS27k
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Comment: C: PDB rotation along parallel axis using biopython
... Could you please add the code for how you determine the structure center? Also, which structure are you using? ...
written 4.4 years ago by Felix_Sim250

Latest awards to Felix_Sim

Scholar 3.0 years ago, created an answer that has been accepted. For A: BioPerl/BioGraphics only prints one value instead of all
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: kegg biopython error in retrieving enzyme record
Good Answer 3.9 years ago, created an answer that was upvoted at least 5 times. For A: Pairwise2 - Biopython - weird local alignment results
Appreciated 4.3 years ago, created a post with more than 5 votes. For A: Pairwise2 - Biopython - weird local alignment results
Scholar 5.0 years ago, created an answer that has been accepted. For A: BioPerl/BioGraphics only prints one value instead of all
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Master in statistics or bioinformatics
Scholar 5.3 years ago, created an answer that has been accepted. For A: BioPerl/BioGraphics only prints one value instead of all
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: Master in statistics or bioinformatics
Scholar 6.1 years ago, created an answer that has been accepted. For A: BioPerl/BioGraphics only prints one value instead of all

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