User: ac.research

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Posts by ac.research

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Comment: A: Sequence extaction using Biopython
... People, this might be an old post, but from Bio import SeqIO does not seem to work. is it depreciated? ...
written 8 hours ago by ac.research0
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Comment: C: Module to RMSD two proteins with Python?
... Hi, I know this might be very late to comment to it, but Bio.SVDSuperimposer does not seem to rotate the proteins to get the lowest RMSD: i get RMSD = 0.2 for chains that when aligned in PyMOL give RMSD = 0.06 here is my code: fixed = Bio.PDB.Selection.unfold_entities(Bio.PDB.Polypeptide.PPBu ...
written 19 hours ago by ac.research0
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Comment: C: Calculate Radius of Gyration [python 3]
... I fixed the PyMol script to make it a stand alone script capable of running on python3 independent of PyMol. Here is a link to it in case someone wants to use it in the future :-) https://github.com/sarisabban/Rg ...
written 5 weeks ago by ac.research0
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Comment: C: Calculate Radius of Gyration [python 3]
... Hmmm, the script from pymol does not work out of the box, but I modified it and it works now. Thanks. But the issue is that I cannot call it from within another python script (in other words I cannot run the script with python3 scriptname.py rather pymol -c scriptname.py) which means I cannot inclu ...
written 5 weeks ago by ac.research0
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Calculate Radius of Gyration [python 3]
... Hello Everyone, I am trying to find a way to calculate the Rg (Radius of Gyration) of a protein. I searched through Biopython but I could not find a way to do it. Is it possible to do this calculation from Biopython? Is there a script someone has written that I can use, even if it uses a library ...
pdb python radius of gyration biopython protein written 5 weeks ago by ac.research0
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Answer: A: How to upload fasta file to SSH Supercomputer
... There is a very simple command: scp from to Example to supercomputer: scp /path/to/your/file username@132.343.12.3:/path/to/your/destination/on/supercomputer scp /home/acresearch/desktop/uniprot90 acresearch@castor:/home/acresearch/databses Example from supercomputer: scp userna ...
written 3 months ago by ac.research0
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Comment: C: PSIPRED, how to install and make it work?
... It works now, I had an issue with the makeblastdb command (a typo as you said). Thank you very much. ...
written 3 months ago by ac.research0
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Comment: C: PSIPRED, how to install and make it work?
... I changed the commands to the following: wget ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz gunzip -v uniref90.fasta.gz makeblastdb -in uniref90.fasta -dbtype prot -input_type fasta -out uniref90.fasta And the database seems to setup ok (no errors printe ...
written 3 months ago by ac.research0
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Comment: C: PSIPRED, how to install and make it work?
... Thank you for your replay. I think the problem I am facing is with the database setup, these are the steps I follow to setup the UniProt90 database (slightly changed from the top and without using pfilt as you advised): wget ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90. ...
written 3 months ago by ac.research0
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Comment: C: PSIPRED, how to install and make it work?
... I followed these instructions, but they are 4 years old and it seems there has been major changes to the PSIPRED program as well as others. Hence the steps in that forum entry do not work anymore. ...
written 3 months ago by ac.research0

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